http://wiki.c2b2.columbia.edu/workbench/api.php?action=feedcontributions&feedformat=atom&user=Ginhoven 2026-04-30T14:32:40Z User contributions MediaWiki 1.27.7 http://wiki.c2b2.columbia.edu/workbench/index.php?title=Array_Sets&diff=3284 2006-07-06T20:16:48Z

<p>Ginhoven: /* Assigning arrays to sets */</p> <hr /> <div>{{TutorialsTopNav}}<br /> <br /> ==Outline==<br /> In this tutorial, you will learn<br /> <br /> *How geWorkbench allows sets of markers and arrays/phenotypes to be defined and created.<br /> *How to create a set of arrays<br /> *How to mark a set of arrays as &quot;Active&quot;<br /> *How to classify a set of arrays, e.g. as &quot;case&quot; vs. &quot;control&quot;.<br /> *How arrays can be grouped in different ways with descriptive tags.<br /> <br /> <br /> ==Background==<br /> <br /> geWorkbench makes extensive use of the notion of sets of markers or arrays/phenotypes. Sets of markers are returned from various analysis routines. Sets of arrays/phenotypes can be specified to group arrays in a meaningful fashion for statistical analysis. For example, two such phenotypes might be the diseased and normal states of a tissue from which samples have been taken. <br /> <br /> geWorkbench supports groupings of sets. Each such group can contain different sets of markers or arrays.<br /> <br /> Sets of markers can also be created by various components of geWorkbench. For example the t-test returns a list of markers showing signficant differential expression, and after hierarchical clustering, the markers in a subtrees of the resulting dendrogram can be saved to a list. The examples below will focus on creating sets of arrays/phenotypes. As mentioned, examples of creating and working with sets of markers can be found in [[Tutorial_-_Differential_Expression]] and [[Tutorial_-_Clustering]].<br /> <br /> <br /> ==Preparation==<br /> <br /> In this tutorial we will start with the same data files that were used in [[Tutorial - Projects and Data Files]]. Load the ten individual MAS5 data files as shown there in the section &quot;Creating a new project and loading microarray data files&quot;.<br /> <br /> ==Assigning arrays to sets==<br /> <br /> We will place the arrays in the default group, however you can create a new group by pushing the '''New''' button on '''Array/Phenotype Sets''' at lower left.<br /> <br /> First, we will select and label arrays which contain samples from the congestive cardiomyopathy disease state:<br /> <br /> 1. In the Arrays/Phenotypes component, select the six arrays beginning with '''JB-ccmp''', which represent the samples from the congestive cardiomyopathy disease state.<br /> <br /> [[Image:T_Arrays_AddToSet.png]]<br /> 2. Right-click, select '''Add to Set'''.<br /> <br /> <br /> 3. Enter &quot;CCMP&quot; in the input box and click OK.<br /> <br /> [[Image:T_Arrays_SetLabel.png]]<br /> <br /> <br /> 4. Next, similarly label the arrays beginning with JB-n as &quot;Normal&quot; ('' repeat steps 2 &amp; 3 ''):<br /> <br /> The Array/Phenotype Sets component will now show the two sets added:<br /> <br /> [[Image:T_Array_ArraySets.png]]<br /> <br /> ==Activating sets==<br /> <br /> The check boxes next to the set name can be checked to indicate that a sets of arrays is &quot;Active&quot;. Various analysis and visualization components can be set to only use/display activated arrays or markers.<br /> <br /> <br /> [[Image:T_Arrays_ActivateSets.png]]<br /> <br /> <br /> ==Classifying a set==<br /> <br /> For statistical tests such as the t-test, Case and Control groups can be specified. <br /> <br /> # Left-click on the thumb-tack icon in front of the phenotype name. <br /> # Select Case to specify the disease arrays as the &quot;Case&quot;. The remaining &quot;Normal&quot; arrays are by default labeled control.<br /> <br /> [[Image:T_Arrays_SetCase.png]]<br /> <br /> <br /> A red thumbtack indicates the arrays have been specified as &quot;Case&quot;.<br /> <br /> <br /> [[Image:T_Arrays_CaseSet.png]]<br /> <br /> <br /> ==Example of using multiple array groups==<br /> <br /> There can be different groupings of the same arrays in the Arrays/Phenotypes and Marker components. Here we show how there are several different groupings defined in the example data file &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot;. After loading this file into geWorkbench as type &quot;Affymetrix File Matrix&quot;, the following groups can be seen in the Arrays/Phenotypes group pulldown menu:<br /> <br /> [[Image:T_Arrays_Groups_choose.png]]<br /> <br /> <br /> If we choose the group called &quot;Class&quot;, the following sets of arrays are displayed:<br /> <br /> [[Image:T_Arrays_Groups_Class.png]]<br /> <br /> <br /> If instead we choose the group &quot;Cell Line&quot;, a different grouping of the same arrays is seen:<br /> <br /> [[Image:T_Arrays_Groups_CellLine.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=Workspace&diff=3283 2006-07-06T16:16:22Z

<p>Ginhoven: /* Workspaces and Projects */</p> <hr /> <div>{{TutorialsTopNav}}<br /> <br /> ==Outline==<br /> In this tutorial, you will learn how to: <br /> <br /> *Create a new Project.<br /> *Load microarray data.<br /> *Merge data from several loaded microarray experiments.<br /> *Rename a project and/or project node.<br /> *Remove a project and/or project node.<br /> *Save project files that you have created.<br /> *Load, add, and/or modify remote data.<br /> <br /> <br /> <br /> ==Supported data formats==<br /> *Microarray<br /> **Affymetrix MAS5/GCOS files - produced by the Affymetrix data analysis programs.<br /> **Affymetrix File Matrix - a spreadsheet-type multi-experiment format; this is the native file type created by geWorkbench from merged datasets.<br /> **Tab-delimited text (RMAExpress file) - A simple columnar file format, produced by the program RMAExpress.<br /> **Affy Excel or txt data file - formats for single Affymetrix experiments (not supported).<br /> **Genepix files - Produced by a popular analysis program for two-color microarrays.<br /> *Other<br /> **FASTA files. DNA or amino-acid sequence files in FASTA format.<br /> **Pattern files - sequence motifs produced using the Pattern Discovery component of geWorkbench.<br /> **Genotypic data files - (not supported).<br /> <br /> <br /> ==Data organization==<br /> <br /> ===Workspaces and Projects===<br /> In the '''Project Folders''' component there is a top-level object called a workspace. The workspace can contain one or more separate projects, and each project can contain opened data files and analysis results. The workspace as a whole, with all its projects and data nodes, can be saved and restored. Projects allow data to be grouped, for example by experiment. A project can contain many different types of data, for example microarray data, fasta sequence files and graphical images.<br /> <br /> ===Microrray data and merging===<br /> A file from disk or from the network is be opened within a given project. Creation of a new project is described below. When working with microarray data, all data to be analyzed must be present within one data node in a project. If the data exists as multiple files containing results from single arrays, the data must be merged into a single node before it can be used. geWorkbench can perform this merging step either at the time data is read in, or later in a separate step. Once merged, such a dataset can be saved out to disk; it will be saved in the geWorkbench matrix file format.<br /> <br /> <br /> ==Limitations==<br /> Only one data node can be selected at one time. If you wish to save a data node to a file, in most cases you must specify a file type extension, such as &quot;.exp&quot; for the geWorkbench merged file matrix format, or &quot;.fasta&quot; for a sequence file. At present, the only type of remote data source which can be opened is NCICB's caArray database. The remote file open feature is not multi-threaded, so you cannot perform other tasks in geWorkbench while downloading remote files.<br /> <br /> <br /> <br /> ==Creating a new project and loading microarray data files==<br /> <br /> <br /> In this example, we will load 10 individual Affymetrix MAS5 format files, and merge them into a single dataset. The origin of these file is described in the section [[Tutorial_-_Data]]<br /> <br /> All data must belong to a project. Right-click on the '''Workspace''' entry in the '''Project Folders''' window at upper left to create a new project.<br /> <br /> [[Image:T_NewProject.png]]<br /> <br /> <br /> <br /> Next, right-click on the '''New Project''' entry and select '''Open Files'''.<br /> <br /> [[Image:T_OpenFiles.png]]<br /> <br /> <br /> Here, we will select file type '''Affymetrix GCOS/MAS5''' as shown.<br /> <br /> Make sure to check the '''Merge files''' checkbox. This will created the merged data node as the files are read in.<br /> <br /> We will select 10 MAS5 format text files from the directory geworkbench\data\training\cardiogenomics.med.harvard.edu, which is included in the geWorkbench download. <br /> <br /> Click '''Open'''.<br /> <br /> [[Image:T_OpenFile_CardioMerge.png]]<br /> <br /> <br /> <br /> You may see the message &quot;The chip type HG_U95Av2 is recognized...&quot;<br /> <br /> [[Image:T_OpenFile_ChipRecog.png]]<br /> <br /> <br /> <br /> The merged dataset is listed in the Project folder. The data is displayed, in single array format, in the '''Microarray Viewer'''. Note we have increased the intensity slider to maximum here. You can scroll through the arrays from first to last using the slider. The display in the '''Microarray Viewer''' is by marker in the linear order the markers appear in the data file. It does not correspond in any way to a physical picture or representation of the actual 2-D microarray.<br /> <br /> [[Image:T_FullApp_MergedData.png]]<br /> <br /> <br /> ==Merging microarray datafiles after they have already been loaded.==<br /> <br /> If Affymetrix data files are not merged at the time they are read in, they can also be merged later, as long as they are from the same chip type.<br /> <br /> <br /> '''1.''' Select the read-in data files that you want to merge.<br /> <br /> '''2.''' Click on '''File''' in the menu bar, and choose '''Merge Datasets'''.<br /> <br /> The picture shows the resulting merged dataset created from several individual data files.<br /> <br /> [[Image:T_ProjectFolder_MergeIndivid.png]]<br /> <br /> <br /> The result is a new data node containing the merged data. The original data nodes are still present.<br /> <br /> [[Image:T_ProjectFolder_IndividMerged.png]]<br /> <br /> <br /> ==Renaming a project or a data node==<br /> <br /> <br /> ===Renaming a project===<br /> <br /> '''1.''' Right-click on '''Project''' folder.<br /> <br /> '''2.''' Select '''Rename'''.<br /> <br /> <br /> [[Image:T_ProjectFolder_RenameProject.png]] <br /> <br /> <br /> '''3.''' In the pop-up screen rename your project.<br /> <br /> '''4.''' Click on the '''OK''' button<br /> <br /> <br /> ===Renaming a project data node===<br /> <br /> '''1.''' Right-click on a Project Folder data node.<br /> <br /> '''2.''' Select '''Rename'''.<br /> <br /> [[Image:T_ProjectFolder_RenameDataset.png]]<br /> <br /> <br /> <br /> '''3.''' In the pop-up screen rename your data node.<br /> <br /> [[Image:T_ProjectFolder_RenameDataset2.png]]<br /> <br /> <br /> '''4.''' Click on the '''OK''' button.<br /> <br /> <br /> <br /> ==Removing a project or a data node==<br /> <br /> ===Removing a project===<br /> <br /> '''1.''' Right-click on '''Project''' folder.<br /> <br /> '''2.''' Select '''Remove'''.<br /> <br /> <br /> <br /> ===Removing a project data node===<br /> <br /> '''1.''' Right-click on the data node.<br /> <br /> '''2.''' Select '''Remove'''. <br /> <br /> <br /> ==Saving a data node to a file==<br /> <br /> It is here that, among other things, you can create the matrix multi-experiment file format used by geWorkbench from a merged dataset.<br /> <br /> '''1.''' Right-click on data node that you want to save. <br /> <br /> '''2.''' Click '''Save'''.<br /> <br /> [[Image:T_ProjectFolder_SaveNode.png]]<br /> <br /> <br /> A standard file '''Save''' screen will come up.<br /> <br /> '''3.''' Choose a location.<br /> <br /> '''4.''' Enter a name. Here you should be careful to enter an appropriate file type extension. as this is not automatic. For example for the merged multi-experiment matrix file type you should include the extension &quot;.exp&quot; in the filename.<br /> <br /> '''5.''' Click on the '''Save''' button.<br /> <br /> <br /> ==Working with remote data sources==<br /> <br /> ===The remote Open File dialog===<br /> geWorkbench can retrieve data from certain remote data sources; currently only instances of the NCICB's caArray database are supported. The Open File dialog allows remote sources to be added to the list of those available either manually or through discovery using grid services. Entries (locations, parameters) for non-grid services can be edited.<br /> <br /> As before, right-click on '''Project''' which will bring up the '''Open File''' dialog. Click the '''Remote''' radio button. The '''Open File''' dialog window will be expanded to include remote sources.<br /> <br /> Note the distinction between the &quot;Open File&quot; button, which opens a local or remote file, and the &quot;Go&quot; button, described below, which connects to a chosen remote resource to allow browsing.<br /> <br /> [[Image:(T)MEditRemoteData.png]]<br /> <br /> Four additional buttons appear. They are: <br /> <br /> '''caArray''' button - lists remote resources.<br /> <br /> '''Go''' button - connects to the selected remote source.<br /> <br /> '''Add A New Resource''' button - Opens the Data Source Definition Page used to add a remote data source.<br /> <br /> '''Edit''' button - Edits remote source parameters.<br /> <br /> <br /> ===Loading data from a remote instance of caArray===<br /> <br /> Click on the '''Go''' button next to the caArray data source at the bottom of the dialog. All available caArray experiments at that location will be displayed.<br /> <br /> [[Image:T_ProjectFolder_caArrayExpts.png]]<br /> <br /> Note that the type of experiment data provided here in caArray is of type &quot;derived bioassay&quot;. This is data that has been processed from raw data, for example using RMA.<br /> <br /> Select an experiment that has derived bioassays. Here we depict the experiment ending in *99049. The number of derived bioassays, 12, is displayed, along with the experiment information. (A new dataset, &quot;Public Rembrandt&quot; has subsequently been added, which would also be good to use for experimenting with caArray data download. It has 53 bioassays available).<br /> <br /> To retrieve the bioassays themselves, right click on the experiment and press '''Get bioassays'''. This will download the list of available bioassays into geWorkbench.<br /> <br /> [[Image:T_ProjectFolder_GetRemoteBioassays.png]]<br /> <br /> <br /> To actually retrieve bioassay data, select one or more desired arrays and push the '''Open''' button. (Although below we show retrieving multiple array datasets, for demonstration purposes you might want to first select just one, as each can take several minutes to download).<br /> <br /> You can either select the merge option here, or wait until all data has been successfully download to perform a merge later.<br /> <br /> Note that downloading data from a remote resource is not multi-threaded, so you will not be able to perform other actions in geWorkbench while the data is downloaded.<br /> <br /> [[Image:T_ProjectFolder_OpenRemoteBioassays.png]]<br /> <br /> ===To add a remote source===<br /> <br /> (Note - currently only caArray data sources are supported).<br /> <br /> '''1.''' Click on the '''Add A New Resource''' button.<br /> <br /> [[Image:(T)MRemoteData2.png]]<br /> This is the Data Source Definition Page<br /> <br /> '''2.''' Fill in the Data Source definition page. URL and Short Name are required fields.<br /> <br /> '''3.''' Click on the OK button.<br /> <br /> The configuration is set up to automatically reflect your additional Data Source.<br /> <br /> <br /> ===To modify a remote source===<br /> <br /> The specification of the remote resource can be edited.<br /> <br /> '''1.''' Click on the '''Edit''' button at the bottom of the '''Open File''' dialog.<br /> <br /> '''2.''' Make the changes that you need.<br /> <br /> '''3.''' Click on the '''OK''' button<br /> <br /> [[Image:T_ProjectPanel_EditRemote.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=Tutorial_-_Reverse_Engineering&diff=3280 2006-06-23T17:34:21Z

<p>Ginhoven: /* Overview */</p> <hr /> <div>{{TutorialsTopNav}}<br /> <br /> <br /> ==Overview==<br /> The Reverse Engineering component included in geWorkbench is being rewritten (as of April 2006), and hence in a future release the details of the interface may change. However, the functionality will be similar.<br /> <br /> The primary use of the Reverse Engineering component is to infer regulatory interactions between genes and gene products. The Reverse Engineering component uses the information theory concept of mutual information to find these interactions. Mutual Information is in principle more sensitive and flexible than a simple correlation calculation. It is also invariant under data transformations, so the details of normalization should not be important.<br /> <br /> ==Reverse Engineering in the context of geWorkbench==<br /> The Reverse Engineering component calculates the information that the expression pattern of one gene carries about the expression of another gene, that is, it is a pairwise calculation. Larger datasets, containing more arrays per marker, will yield greater sensitivity and better statistical support. Full scale runs of reverse engineering algorithms, comparing all markers against each other, and typically done on datasets containing several hundred microarrays, are typically performed on large cluster computers and are not feasible on a desktop machine. During 2006 we hope to provide a remote service that can host such calculations for jobs launched from geWorkbench. However, at present, smaller scale calculations are supported directly in geWorkbench.<br /> <br /> As typically used in geWorkbench, the Reverse Engineering component calculates the Mutual Information score between a single hub gene and all other N markers in the dataset. In a second step, a subset containing the best M markers is chosen (with a current limit of 100), and a complete pairwise MxM/2 mutual information calculation is performed between them. The network resulting from this calculation can be displayed as a branched tree of interactions within the Cytoscape component.<br /> <br /> ==Prerequisites==<br /> A dataset containing multiple arrays (the more the better) should be loaded into geWorkbench. If data is loaded from separate files, it should be merged into a single microarray datset, either at the time of or after being read in. See the section [[Tutorial - Projects and Data Files | Projects and Data Files]]. In this tutorial we will load a dataset also used in other tutorial sections, which has been normalized, and filtered to reduce the number of genes. This file, &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot; will be made available in the tutorial data section. It can also be obtained by starting with the file &quot;webmatrix.exp&quot; available in the ''downloads'' section and performing the following steps:<br /> <br /> 1. Load the file webmatrix.exp.<br /> <br /> 2. Quantile Normalize.<br /> <br /> 3. Log2 transform (also in the Normalize tab).<br /> <br /> 4. Filter out values having deviation less than 1.<br /> <br /> 5. Remove markers with filtered-out values using the missing values filter with a threshold of 0.<br /> <br /> ==Example - Profiler==<br /> * Load the data file &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot;. This contains a set of 100 experiments on Affymetrix HG_U95Av2 chips. As described above, this file has been quantile normalized, log2 converted, and then filtered to remove markers with a deviation of less than 1, in order to reduce the size of the dataset, leaving 3837 markers.<br /> <br /> * In the upper right section of geWorkbench find the Reverse Engineering component. It should by default be displaying the '''Profiler''' tab.<br /> <br /> * In the Markers component search box, on the left side of the geWorkbench interface, enter 1973 and hit enter. This will find the marker 1973_s_at, which is the c-Myc gene, a well-known transcription factor with many interactions. Click on this marker in the list. This will enter the marker into the '''Hub Gene Label''' field of the '''Profiler'''.<br /> <br /> <br /> [[Image:T_Markers_Search1973.png]]<br /> <br /> <br /> * The default setting in the Profiler is '''Mutual Information (fast)'''. With this selected, hit '''Analyze(2D)'''. This will return a list of all markers having a MI score of greater than the cutoff value (the default is 0.2).<br /> <br /> <br /> [[Image:T_ReverseEngineering_Basic.png]]<br /> <br /> <br /> After the Mutual Information algoritnm has been run, an adjacency matrix will be placed in the Projects Folder:<br /> <br /> <br /> [[Image:T_ProjectFolders_AdjacencyMatrix.png]]<br /> <br /> <br /> * If at this point you hit the Create Network button, a network will be displayed based on the top 100 markers interacting with c-Myc. As described above, the MI algoritm is run again on these M=100 markers, in order to measure interactions between each pair. Each marker is then connected via an edge with the marker it most strongly interacts with, with the chosen hub-gene at the center.<br /> <br /> <br /> [[Image:T_ReverseEngineering_InitialNet.png]]<br /> <br /> <br /> This is best seen in '''Cytoscape''' by going to the '''Layout''' menu, and chosing '''yFiles-&gt;organic'''. The layout will now appear as:<br /> <br /> <br /> [[Image:T_ReverseEngineering_Central1973.png]]<br /> <br /> <br /> * If a smaller list is desired, a set of markers can be highlighted in the list originally returned. Only this selected subset, up to 100 markers, will then be used if &quot;Create Network&quot; is pressed.<br /> <br /> * By right-clicking and selecting &quot;Add to Set&quot;, this group will be added to the '''Markers''' component as a new set of markers which can be used in other components (sequence retrieval, annotation retriever etc.).<br /> <br /> * Within the network created in Cytoscape, one can select the central gene, and then on the '''Cytoscape''' menu chose '''Select-&gt;Nodes-&gt;First Neighbors''' of selected nodes. <br /> <br /> [[Image:T_ReverseEngineering_SelectFirstNeighbors.png]]<br /> <br /> <br /> The first neighbors will be highlighted in the graph, <br /> <br /> <br /> [[Image:T_ReverseEngineering_FirstNeighbors.png]]<br /> <br /> <br /> and also added as a new set in the '''Markers''' component.<br /> <br /> <br /> [[Image:T_Markers_ReverseEng_Selected.png]]<br /> <br /> <br /> We can return to the main Reverse Engineering component by clicking on the original dataset in the Project Folders component. If we select the first (highest MI score) marker on the list, the graph shown below is drawn in the '''Motif Location Histogram''' display. This shows a plot of the expression values on each array for the selected hub marker vs any other marker selected in the list.<br /> <br /> <br /> [[Image:T_ReverseEngineering_MotifHistogram.png]]<br /> <br /> ==Options==<br /> <br /> '''Pearson''' - Uses a Pearson correlation function to calculate the interaction scores.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=SOM&diff=3276 2006-06-16T14:43:17Z

<p>Ginhoven: /* Background */</p> <hr /> <div>{{TutorialsTopNav}}<br /> <br /> __TOC__<br /> <br /> ==Note==<br /> <br /> The algorithm use for Fast Hierarchical Clustering analysis does not implement the commonly understood versions of Average Linkage and Total Linkage. This problem is present in the current version (1.0.3) of geWorkbench and all previous versions. Standard implementations will be available in the next release. The implementation of single linkage gives results as expected from the standard algorithm.<br /> <br /> ==Outline==<br /> <br /> In this section the following information about clustering methods is covered:<br /> # What clustering is and how it can be used.<br /> # Methods implemented in geWorkbench: SOMs and Hierarchical Clustering<br /> # An example of performing an SOM analysis<br /> # An example of performing a Hierarchical Clustering analysis.<br /> <br /> <br /> ==Background==<br /> <br /> Clustering methods can allow identification of groups of markers with similar expression. A common application is to search for genes that appear to be co-regulated. A list of such markers, saved to the '''Markers''' component, can be used for further steps, such as retrieving upstream sequences, Gene Ontology analysis, or viewing of annotations.<br /> <br /> ==Methods supported==<br /> <br /> geWorkbench supports two clustering methods:<br /> # Self-Organizing maps (SOMs)<br /> # Hierarchical Clustering<br /> <br /> Self-organizing maps group the markers into a user-specified number of bins. In geWorkbench, a SOM visualizer component displays the results graphically. Hierarchical clustering constructs a tree-like relationship among the expression patterns of all markers present. Results are viewed in the Dendrogram component.<br /> <br /> ==SOM Example==<br /> <br /> * Load the microarray dataset &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot;, available in the tutorial_data.zip [[Download]]. <br /> * In the '''Arrays/Phenotypes''' component pulldown menu, select the group labeled &quot;Class&quot;.<br /> * Activate two sets of arrays to compare, e.g. GC B-cell and non-GC B-cell, by checking the boxes before the names (these are chosen here because they are the smallest groups).<br /> * Go to the '''Analysis''' component, and select '''SOM Analysis'''.<br /> <br /> Parameters:<br /> Rows, Columns - give the number of bins into which to separate the different marker expression patterns.<br /> Radius - <br /> Iterations - <br /> Alpha - <br /> Function - Bubble or Gaussian<br /> <br /> The default parameters are shown below. We will accept these parameters.<br /> <br /> [[Image:T_SOM_Analysis_Parameters.png]]<br /> <br /> <br /> The resulting display of nine clusters is shown below. The user should experiment with different parameters to attempt to discern informative groupings.<br /> <br /> <br /> [[Image:T_SOM_display.png]]<br /> <br /> <br /> Any individual graph can be right-clicked on and &quot;Add to Set&quot; chosen. This will add these markers to a new Set in the '''Markers''' component. Each will be given a name starting with &quot;Cluster Grid&quot; and the number of markers will be shown.<br /> <br /> ==Hierarchical Clustering - Example==<br /> <br /> * Load the microarray dataset &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot;, available in the tutorial_data.zip [[Download]]. <br /> * In the Arrays/Phenotypes component, select the set of arrays labeled &quot;Class&quot;.<br /> * Activate two classes of arrays to compare, e.g. GC B-cell and non-GC B-cell, by checking the boxes before the names.<br /> * Go to the Analysis component, and select Hierarchical Clustering.<br /> * At the bottom of the Analysis component, the box that says '''All Arrays''' should be unchecked, so that the array selection above is used.<br /> <br /> <br /> * In Hierarchical Clustering, set the parameters to:<br /> ** Clustering Method: Total Linkage<br /> ** Clustering Dimension: Both<br /> ** Clustering Metric: Euclidean<br /> <br /> *Click '''Analyze'''.<br /> <br /> The results will be displayed in the Dendrogram component.<br /> <br /> [[Image:T_HierarchicalClustering_BCregion.png]]<br /> <br /> By scrolling down a bit, one finds a large interesting area, showing clear differences between groups of arrays. We will select two clearly differentiated clusters. Check the '''Enable Zoom''' checkbox. Then highlight the first cluster of 12 markers as shown here:<br /> <br /> [[Image:T_HierarchicalClustering_BC12Markers.png]]<br /> <br /> <br /> Then left-click to select this subset of the dendrogram. It will be displayed alone. <br /> <br /> [[Image:T_HierarchicalClustering_BC12MarkersZoom.png]]<br /> <br /> <br /> Now right-click and select &quot;Add to Set&quot;. In the Markers component, the select genes are added as Cluster Tree [12], where 12 is the number of markers selected.<br /> <br /> <br /> Repeat for the similar region just below, which contains another 44 markers.<br /> <br /> <br /> [[Image:T_HierarchicalClustering_BC44Markers.png]]<br /> <br /> <br /> This will result in two sets of markers having been added to the Markers component, as shown below:<br /> <br /> [[Image:T_Markers_ClusterTree12and44.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=Tutorial_-_Reverse_Engineering&diff=3138 2006-06-02T20:57:47Z

<p>Ginhoven: /* Reverse Engineering in the context of geWorkbench */</p> <hr /> <div>{{TutorialsTopNav}}<br /> <br /> <br /> ==Overview==<br /> The Reverse Engineering component included in geWorkbench is being rewritten (as of April 2006), and hence in a future release the details of the interface may change. However, the functionality will be similar.<br /> <br /> The primary use of the Reverse Engineering component is to infer regulatory interactions between genes and gene products. The Reverse Engineering component uses the information theory concept of mutual information to find these interactions. Mutual Information is in principle more senstive and flexible than a simple correlation calculation. It is also invariant under data transformations, so the details of normalization should not be important.<br /> <br /> <br /> ==Reverse Engineering in the context of geWorkbench==<br /> The Reverse Engineering component calculates the information that the expression pattern of one gene carries about the expression of another gene, that is, it is a pairwise calculation. Larger datasets, containing more arrays per marker, will yield greater sensitivity and better statistical support. Full scale runs of reverse engineering algorithms, comparing all markers against each other, and typically done on datasets containing several hundred microarrays, are typically performed on large cluster computers and are not feasible on a desktop machine. During 2006 we hope to provide a remote service that can host such calculations for jobs launched from geWorkbench. However, at present, smaller scale calculations are supported directly in geWorkbench.<br /> <br /> As typically used in geWorkbench, the Reverse Engineering component calculates the Mutual Information score between a single hub gene and all other N markers in the dataset. In a second step, a subset containing the best M markers is chosen (with a current limit of 100), and a complete pairwise MxM/2 mutual information calculation is performed between them. The network resulting from this calculation can be displayed as a branched tree of interactions within the Cytoscape component.<br /> <br /> ==Prerequisites==<br /> A dataset containing multiple arrays (the more the better) should be loaded into geWorkbench. If data is loaded from separate files, it should be merged into a single microarray datset, either at the time of or after being read in. See the section [[Tutorial - Projects and Data Files | Projects and Data Files]]. In this tutorial we will load a dataset also used in other tutorial sections, which has been normalized, and filtered to reduce the number of genes. This file, &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot; will be made available in the tutorial data section. It can also be obtained by starting with the file &quot;webmatrix.exp&quot; available in the ''downloads'' section and performing the following steps:<br /> <br /> 1. Load the file webmatrix.exp.<br /> <br /> 2. Quantile Normalize.<br /> <br /> 3. Log2 transform (also in the Normalize tab).<br /> <br /> 4. Filter out values having deviation less than 1.<br /> <br /> 5. Remove markers with filtered-out values using the missing values filter with a threshold of 0.<br /> <br /> ==Example - Profiler==<br /> * Load the data file &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot;. This contains a set of 100 experiments on Affymetrix HG_U95Av2 chips. As described above, this file has been quantile normalized, log2 converted, and then filtered to remove markers with a deviation of less than 1, in order to reduce the size of the dataset, leaving 3837 markers.<br /> <br /> * In the upper right section of geWorkbench find the Reverse Engineering component. It should by default be displaying the '''Profiler''' tab.<br /> <br /> * In the Markers component search box, on the left side of the geWorkbench interface, enter 1973 and hit enter. This will find the marker 1973_s_at, which is the c-Myc gene, a well-known transcription factor with many interactions. Click on this marker in the list. This will enter the marker into the '''Hub Gene Label''' field of the '''Profiler'''.<br /> <br /> <br /> [[Image:T_Markers_Search1973.png]]<br /> <br /> <br /> * The default setting in the Profiler is '''Mutual Information (fast)'''. With this selected, hit '''Analyze(2D)'''. This will return a list of all markers having a MI score of greater than the cutoff value (the default is 0.2).<br /> <br /> <br /> [[Image:T_ReverseEngineering_Basic.png]]<br /> <br /> <br /> After the Mutual Information algoritnm has been run, an adjacency matrix will be placed in the Projects Folder:<br /> <br /> <br /> [[Image:T_ProjectFolders_AdjacencyMatrix.png]]<br /> <br /> <br /> * If at this point you hit the Create Network button, a network will be displayed based on the top 100 markers interacting with c-Myc. As described above, the MI algoritm is run again on these M=100 markers, in order to measure interactions between each pair. Each marker is then connected via an edge with the marker it most strongly interacts with, with the chosen hub-gene at the center.<br /> <br /> <br /> [[Image:T_ReverseEngineering_InitialNet.png]]<br /> <br /> <br /> This is best seen in '''Cytoscape''' by going to the '''Layout''' menu, and chosing '''yFiles-&gt;organic'''. The layout will now appear as:<br /> <br /> <br /> [[Image:T_ReverseEngineering_Central1973.png]]<br /> <br /> <br /> * If a smaller list is desired, a set of markers can be highlighted in the list originally returned. Only this selected subset, up to 100 markers, will then be used if &quot;Create Network&quot; is pressed.<br /> <br /> * By right-clicking and selecting &quot;Add to Set&quot;, this group will be added to the '''Markers''' component as a new set of markers which can be used in other components (sequence retrieval, annotation retriever etc.).<br /> <br /> * Within the network created in Cytoscape, one can select the central gene, and then on the '''Cytoscape''' menu chose '''Select-&gt;Nodes-&gt;First Neighbors''' of selected nodes. <br /> <br /> [[Image:T_ReverseEngineering_SelectFirstNeighbors.png]]<br /> <br /> <br /> The first neighbors will be highlighted in the graph, <br /> <br /> <br /> [[Image:T_ReverseEngineering_FirstNeighbors.png]]<br /> <br /> <br /> and also added as a new set in the '''Markers''' component.<br /> <br /> <br /> [[Image:T_Markers_ReverseEng_Selected.png]]<br /> <br /> <br /> We can return to the main Reverse Engineering component by clicking on the original dataset in the Project Folders component. If we select the first (highest MI score) marker on the list, the graph shown below is drawn in the '''Motif Location Histogram''' display. This shows a plot of the expression values on each array for the selected hub marker vs any other marker selected in the list.<br /> <br /> <br /> [[Image:T_ReverseEngineering_MotifHistogram.png]]<br /> <br /> ==Options==<br /> <br /> '''Pearson''' - Uses a Pearson correlation function to calculate the interaction scores.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=Tutorial_-_Reverse_Engineering&diff=3136 2006-06-02T18:54:53Z

<p>Ginhoven: /* Reverse Engineering in the context of geWorkbench */</p> <hr /> <div>{{TutorialsTopNav}}<br /> <br /> <br /> ==Overview==<br /> The Reverse Engineering component included in geWorkbench is being rewritten (as of April 2006), and hence in a future release the details of the interface may change. However, the functionality will be similar.<br /> <br /> The primary use of the Reverse Engineering component is to infer regulatory interactions between genes and gene products. The Reverse Engineering component uses the information theory concept of mutual information to find these interactions. Mutual Information is in principle more senstive and flexible than a simple correlation calculation. It is also invariant under data transformations, so the details of normalization should not be important.<br /> <br /> <br /> ==Reverse Engineering in the context of geWorkbench==<br /> The Reverse Engineering component calculates the information that the expression pattern of one gene carries about the expression of another gene, that is, it is a pairwise calculation. Larger datasets, containing more arrays per marker, will yield greater sensitivity and better statistical support. Full scale runs of reverse engineering algorithms, comparing all markers against each other, and typically done on datasets containing several hundred microarrays, are typically performed on large cluster computers and are not feasible on a desktop machine. During 2006 we hope to provide a remote service that can host such caluclations for jobs launched from geWorkbench. However, at present, smaller scale calculations are supported directly in geWorkbench.<br /> <br /> As typically used in geWorkbench, the Reverse Engineering component calculates the Mutual Information score between a single hub gene and all other N markers in the dataset. In a second step, a subset containing the best M markers is chosen (with a current limit of 100), and a complete pairwise MxM/2 mutual information calculation is performed between them. The network resulting from this calculation can be displayed as a branched tree of interactions within the Cytoscape component.<br /> <br /> ==Prerequisites==<br /> A dataset containing multiple arrays (the more the better) should be loaded into geWorkbench. If data is loaded from separate files, it should be merged into a single microarray datset, either at the time of or after being read in. See the section [[Tutorial - Projects and Data Files | Projects and Data Files]]. In this tutorial we will load a dataset also used in other tutorial sections, which has been normalized, and filtered to reduce the number of genes. This file, &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot; will be made available in the tutorial data section. It can also be obtained by starting with the file &quot;webmatrix.exp&quot; available in the ''downloads'' section and performing the following steps:<br /> <br /> 1. Load the file webmatrix.exp.<br /> <br /> 2. Quantile Normalize.<br /> <br /> 3. Log2 transform (also in the Normalize tab).<br /> <br /> 4. Filter out values having deviation less than 1.<br /> <br /> 5. Remove markers with filtered-out values using the missing values filter with a threshold of 0.<br /> <br /> ==Example - Profiler==<br /> * Load the data file &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot;. This contains a set of 100 experiments on Affymetrix HG_U95Av2 chips. As described above, this file has been quantile normalized, log2 converted, and then filtered to remove markers with a deviation of less than 1, in order to reduce the size of the dataset, leaving 3837 markers.<br /> <br /> * In the upper right section of geWorkbench find the Reverse Engineering component. It should by default be displaying the '''Profiler''' tab.<br /> <br /> * In the Markers component search box, on the left side of the geWorkbench interface, enter 1973 and hit enter. This will find the marker 1973_s_at, which is the c-Myc gene, a well-known transcription factor with many interactions. Click on this marker in the list. This will enter the marker into the '''Hub Gene Label''' field of the '''Profiler'''.<br /> <br /> <br /> [[Image:T_Markers_Search1973.png]]<br /> <br /> <br /> * The default setting in the Profiler is '''Mutual Information (fast)'''. With this selected, hit '''Analyze(2D)'''. This will return a list of all markers having a MI score of greater than the cutoff value (the default is 0.2).<br /> <br /> <br /> [[Image:T_ReverseEngineering_Basic.png]]<br /> <br /> <br /> After the Mutual Information algoritnm has been run, an adjacency matrix will be placed in the Projects Folder:<br /> <br /> <br /> [[Image:T_ProjectFolders_AdjacencyMatrix.png]]<br /> <br /> <br /> * If at this point you hit the Create Network button, a network will be displayed based on the top 100 markers interacting with c-Myc. As described above, the MI algoritm is run again on these M=100 markers, in order to measure interactions between each pair. Each marker is then connected via an edge with the marker it most strongly interacts with, with the chosen hub-gene at the center.<br /> <br /> <br /> [[Image:T_ReverseEngineering_InitialNet.png]]<br /> <br /> <br /> This is best seen in '''Cytoscape''' by going to the '''Layout''' menu, and chosing '''yFiles-&gt;organic'''. The layout will now appear as:<br /> <br /> <br /> [[Image:T_ReverseEngineering_Central1973.png]]<br /> <br /> <br /> * If a smaller list is desired, a set of markers can be highlighted in the list originally returned. Only this selected subset, up to 100 markers, will then be used if &quot;Create Network&quot; is pressed.<br /> <br /> * By right-clicking and selecting &quot;Add to Set&quot;, this group will be added to the '''Markers''' component as a new set of markers which can be used in other components (sequence retrieval, annotation retriever etc.).<br /> <br /> * Within the network created in Cytoscape, one can select the central gene, and then on the '''Cytoscape''' menu chose '''Select-&gt;Nodes-&gt;First Neighbors''' of selected nodes. <br /> <br /> [[Image:T_ReverseEngineering_SelectFirstNeighbors.png]]<br /> <br /> <br /> The first neighbors will be highlighted in the graph, <br /> <br /> <br /> [[Image:T_ReverseEngineering_FirstNeighbors.png]]<br /> <br /> <br /> and also added as a new set in the '''Markers''' component.<br /> <br /> <br /> [[Image:T_Markers_ReverseEng_Selected.png]]<br /> <br /> <br /> We can return to the main Reverse Engineering component by clicking on the original dataset in the Project Folders component. If we select the first (highest MI score) marker on the list, the graph shown below is drawn in the '''Motif Location Histogram''' display. This shows a plot of the expression values on each array for the selected hub marker vs any other marker selected in the list.<br /> <br /> <br /> [[Image:T_ReverseEngineering_MotifHistogram.png]]<br /> <br /> ==Options==<br /> <br /> '''Pearson''' - Uses a Pearson correlation function to calculate the interaction scores.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=Tutorial_-_Reverse_Engineering&diff=3135 2006-06-02T18:53:56Z

<p>Ginhoven: /* Prerequisites */</p> <hr /> <div>{{TutorialsTopNav}}<br /> <br /> <br /> ==Overview==<br /> The Reverse Engineering component included in geWorkbench is being rewritten (as of April 2006), and hence in a future release the details of the interface may change. However, the functionality will be similar.<br /> <br /> The primary use of the Reverse Engineering component is to infer regulatory interactions between genes and gene products. The Reverse Engineering component uses the information theory concept of mutual information to find these interactions. Mutual Information is in principle more senstive and flexible than a simple correlation calculation. It is also invariant under data transformations, so the details of normalization should not be important.<br /> <br /> <br /> ==Reverse Engineering in the context of geWorkbench==<br /> The Reverse Engineering component calculates the information that the expression pattern of one gene carries about the expression of another gene, that is, it is a pairwise calculation. Larger datasets, containing more arrays per marker, will yield greater sensitivity and better ststistical support. Full scale runs of reverse engineering algorithms, comparing all markers against each other, and typically done on datasets containing several hundred microarrays, are typically performed on large cluster computers and are not feasible on a desktop machine. During 2006 we hope to provide a remote service that can host such caluclations for jobs launched from geWorkbench. However, at present, smaller scale calculations are supported directly in geWorkbench.<br /> <br /> As typically used in geWorkbench, the Reverse Engineering component calculates the Mutual Information score between a single hub gene and all other N markers in the dataset. In a second step, a subset containing the best M markers is chosen (with a current limit of 100), and a complete pairwise MxM/2 mutual information calculation is performed between them. The network resulting from this calculation can be displayed as a branched tree of interactions within the Cytoscape component.<br /> <br /> <br /> ==Prerequisites==<br /> A dataset containing multiple arrays (the more the better) should be loaded into geWorkbench. If data is loaded from separate files, it should be merged into a single microarray datset, either at the time of or after being read in. See the section [[Tutorial - Projects and Data Files | Projects and Data Files]]. In this tutorial we will load a dataset also used in other tutorial sections, which has been normalized, and filtered to reduce the number of genes. This file, &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot; will be made available in the tutorial data section. It can also be obtained by starting with the file &quot;webmatrix.exp&quot; available in the ''downloads'' section and performing the following steps:<br /> <br /> 1. Load the file webmatrix.exp.<br /> <br /> 2. Quantile Normalize.<br /> <br /> 3. Log2 transform (also in the Normalize tab).<br /> <br /> 4. Filter out values having deviation less than 1.<br /> <br /> 5. Remove markers with filtered-out values using the missing values filter with a threshold of 0.<br /> <br /> ==Example - Profiler==<br /> * Load the data file &quot;webmatrix_quantile_log2_dev1_mv0.exp&quot;. This contains a set of 100 experiments on Affymetrix HG_U95Av2 chips. As described above, this file has been quantile normalized, log2 converted, and then filtered to remove markers with a deviation of less than 1, in order to reduce the size of the dataset, leaving 3837 markers.<br /> <br /> * In the upper right section of geWorkbench find the Reverse Engineering component. It should by default be displaying the '''Profiler''' tab.<br /> <br /> * In the Markers component search box, on the left side of the geWorkbench interface, enter 1973 and hit enter. This will find the marker 1973_s_at, which is the c-Myc gene, a well-known transcription factor with many interactions. Click on this marker in the list. This will enter the marker into the '''Hub Gene Label''' field of the '''Profiler'''.<br /> <br /> <br /> [[Image:T_Markers_Search1973.png]]<br /> <br /> <br /> * The default setting in the Profiler is '''Mutual Information (fast)'''. With this selected, hit '''Analyze(2D)'''. This will return a list of all markers having a MI score of greater than the cutoff value (the default is 0.2).<br /> <br /> <br /> [[Image:T_ReverseEngineering_Basic.png]]<br /> <br /> <br /> After the Mutual Information algoritnm has been run, an adjacency matrix will be placed in the Projects Folder:<br /> <br /> <br /> [[Image:T_ProjectFolders_AdjacencyMatrix.png]]<br /> <br /> <br /> * If at this point you hit the Create Network button, a network will be displayed based on the top 100 markers interacting with c-Myc. As described above, the MI algoritm is run again on these M=100 markers, in order to measure interactions between each pair. Each marker is then connected via an edge with the marker it most strongly interacts with, with the chosen hub-gene at the center.<br /> <br /> <br /> [[Image:T_ReverseEngineering_InitialNet.png]]<br /> <br /> <br /> This is best seen in '''Cytoscape''' by going to the '''Layout''' menu, and chosing '''yFiles-&gt;organic'''. The layout will now appear as:<br /> <br /> <br /> [[Image:T_ReverseEngineering_Central1973.png]]<br /> <br /> <br /> * If a smaller list is desired, a set of markers can be highlighted in the list originally returned. Only this selected subset, up to 100 markers, will then be used if &quot;Create Network&quot; is pressed.<br /> <br /> * By right-clicking and selecting &quot;Add to Set&quot;, this group will be added to the '''Markers''' component as a new set of markers which can be used in other components (sequence retrieval, annotation retriever etc.).<br /> <br /> * Within the network created in Cytoscape, one can select the central gene, and then on the '''Cytoscape''' menu chose '''Select-&gt;Nodes-&gt;First Neighbors''' of selected nodes. <br /> <br /> [[Image:T_ReverseEngineering_SelectFirstNeighbors.png]]<br /> <br /> <br /> The first neighbors will be highlighted in the graph, <br /> <br /> <br /> [[Image:T_ReverseEngineering_FirstNeighbors.png]]<br /> <br /> <br /> and also added as a new set in the '''Markers''' component.<br /> <br /> <br /> [[Image:T_Markers_ReverseEng_Selected.png]]<br /> <br /> <br /> We can return to the main Reverse Engineering component by clicking on the original dataset in the Project Folders component. If we select the first (highest MI score) marker on the list, the graph shown below is drawn in the '''Motif Location Histogram''' display. This shows a plot of the expression values on each array for the selected hub marker vs any other marker selected in the list.<br /> <br /> <br /> [[Image:T_ReverseEngineering_MotifHistogram.png]]<br /> <br /> ==Options==<br /> <br /> '''Pearson''' - Uses a Pearson correlation function to calculate the interaction scores.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2947 2006-04-12T15:56:32Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> '''Provide a little background info about Wilm's tumor. (It was chosen at random).'''<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers component and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. Then you will an idea if the Columbia Machine is processing a lot of queries.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> '''(Should we say anything about e value and bit score in this tutorial?)'''<br /> '''Do we need more details on reading the data output?'''<br /> '''We need to explain more about the output.'''<br /> '''What about the separate page that pops up?'''<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2939 2006-03-29T21:37:57Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> '''Provide a little background info about Wilm's tumor. (It was chosen at random).'''<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers component and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. Then you will an idea if the Columbia Machine is processing a lot of queries.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> '''(Should we say anything about e value and bit score in this tutorial?)'''<br /> '''Do we need more details on reading the data output?'''<br /> '''We need to explain more about the output.'''<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2938 2006-03-29T21:37:20Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> '''Provide a little background info about Wilm's tumor. (It was chosen at random).'''<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers component and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. Then you will an idea if the Columbia Machine is processing a lot of queries.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> '''(Should we say anything about e value and bit score in this tutorial?)'''<br /> '''Do we need more details on reading the data output?'''<br /> '''We need to explain more about the output'''<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2937 2006-03-29T20:22:17Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> '''Provide a little background info about Wilm's tumor. (It was chosen at random).'''<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers component and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. Then you will an idea if the Columbia Machine is processing a lot of queries.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> '''(Should we say anything about e value and bit score in this tutorial?)'''<br /> '''Do we need more details on reading the data output?'''<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2936 2006-03-29T20:19:34Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> '''Provide a little background info about Wilm's tumor. (It was chosen at random).'''<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers component and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> '''(Should we say anything about e value and bit score in this tutorial?)'''<br /> '''Do we need more details on reading the data output?'''<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2935 2006-03-29T20:16:33Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> '''Provide a little background info about Wilm's tumor. (It was chosen at random).'''<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> '''(Should we say anything about e value and bit score in this tutorial?)'''<br /> '''Do we need more details on reading the data output?'''<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2934 2006-03-29T19:21:03Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> '''(Should we say anything about e value and bit score in this tutorial?)'''<br /> '''Do we need more details on reading the data output?'''<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2933 2006-03-29T19:14:25Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Service tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2932 2006-03-29T17:40:46Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.<br /> <br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2931 2006-03-29T17:39:54Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> [[Image:(T)Blast Tutorial5.png]]<br /> <br /> The Load button allows you to load an external Blast file in HTML format into the viewer.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2930 2006-03-29T17:37:56Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.<br /> <br /> [[Image:(T)Blast Tutorial5.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2929 2006-03-29T17:33:52Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results are returned they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2928 2006-03-29T17:33:21Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> '''Note:''' The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]<br /> <br /> <br /> When the results return they are placed in the Project Folders as a child of the sequence they correspond to. You can mouse over the result set to see how many sequences are in it.<br /> <br /> In the Blast results viewer, you can examine the alignments. Each different target hit is listed on a line in the results table.<br /> <br /> In the Blast results viewer you can select sequences to add back to the main project by checking the include box and then the Add Selected Sequences To Your Project tab.<br /> <br /> You can also add just the aligned parts by clicking on the tab Only Add Aligned Parts.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2927 2006-03-29T17:22:40Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> The result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2926 2006-03-29T17:21:18Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> Note: Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2925 2006-03-29T17:20:36Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:(T)Blast_Tutorial5.png&diff=2924 2006-03-29T17:20:00Z

<p>Ginhoven: </p> <hr /> <div></div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2923 2006-03-29T17:14:42Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button, under the Server tab. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2922 2006-03-29T17:13:48Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button. This will give you an idea of how busy the Columbia Machine is.<br /> <br /> [[Image:(T)Blast Tutorial4.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:(T)Blast_Tutorial4.png&diff=2921 2006-03-29T17:12:55Z

<p>Ginhoven: </p> <hr /> <div></div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2920 2006-03-29T17:09:55Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]<br /> <br /> <br /> *Observe the progress bar, Blast is now runnning.<br /> <br /> *You can check the server status by hitting the Refresh button. This will give you an idea of how busy the Columbia Machine is.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2919 2006-03-29T17:07:18Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.<br /> <br /> [[Image:(T)Blast Tutorial3.png]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2918 2006-03-29T17:06:23Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]<br /> <br /> <br /> *Click on the Service tab, select Columbia.<br /> <br /> Note: The text field at the bottom shows that one sequence has been selected. If you have a Fasta file that has multiple sequences, you can select the ones you want in the Markers componenet and activate this selection, letting you search on a subset. You may search on all sequences in a file by clicking the All Markers checkbox.<br /> <br /> *Press the curved arrow submit button.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:(T)Blast_Tutorial3.png&diff=2917 2006-03-29T17:05:54Z

<p>Ginhoven: </p> <hr /> <div></div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2916 2006-03-29T16:41:44Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.<br /> <br /> [[Image:(T)Blast Tutorial2.png ]]</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2915 2006-03-29T16:40:36Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.<br /> <br /> <br /> *Click on the Advanced Options Tab<br /> <br /> *Make sure &quot;dna mat&quot; is selected for the Matrix.<br /> <br /> *Change the Expect Value to 0.01.<br /> <br /> *Leave the box checked for PFP filtering for repeated sequence elements (Paracel Filtering Package).<br /> <br /> *Leave the Display result in your web browser checked.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:(T)Blast_Tutorial2.png&diff=2914 2006-03-29T16:40:06Z

<p>Ginhoven: </p> <hr /> <div></div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2913 2006-03-29T16:18:12Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select '''ncbi/nt''' - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2912 2006-03-29T16:17:15Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a '''nucelotide query''', we want to select a nucleotide query program '''blastn'''.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2911 2006-03-29T16:15:33Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> [[Image:(T)Blast Tutoria1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2910 2006-03-29T16:14:45Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> [[Image:(T)Blast Tutorial1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2909 2006-03-29T16:14:19Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> [[Image:Blast Tutorial1.png]]<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:(T)Blast_Tutoria1.png&diff=2908 2006-03-29T16:13:28Z

<p>Ginhoven: </p> <hr /> <div></div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2907 2006-03-29T16:04:57Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> [[Image:(T)Blast Tutorial.png]]<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one) due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> 'insert screen shot here'<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:(T)Blast_Tutorial.png&diff=2906 2006-03-29T15:58:36Z

<p>Ginhoven: </p> <hr /> <div></div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2896 2006-03-24T20:25:18Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> 'insert screen shot here'<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one)due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> 'insert screen shot here'<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2895 2006-03-24T20:19:09Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast tab.<br /> <br /> 'insert screen shot here'<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one)due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> 'insert screen shot here'<br /> <br /> <br /> *Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.<br /> <br /> * Click on the Blast button.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2894 2006-03-24T20:17:34Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast button.<br /> <br /> 'insert screen shot here'<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one)due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> 'insert screen shot here'<br /> <br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here select ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2893 2006-03-24T20:08:09Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast button.<br /> <br /> 'insert screen shot here'<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one)due to the sample.<br /> <br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.<br /> <br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program blastn.<br /> <br /> 'insert screen shot here'<br /> <br /> <br /> Now that the program has been selected, make sure the appropriate databases are displayed (you need to verify this for all algorithms). Here we will try ncbi/nt - the complete non-redundant nucleotide database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2892 2006-03-24T19:50:25Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> 'insert screen shot here'<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast button.<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one)due to the sample.<br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program such as blastn.<br /> <br /> 'insert screen shot here'<br /> <br /> There are five different types of queries you can run, depending on what data you are using:<br /> <br /> '''blastp'''- Compares an amino acid query sequence against a protein sequence database.<br /> <br /> '''blastn'''- Compares a nucleotide query sequence against a nucleotide sequence database.<br /> <br /> '''blastx'''- Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.<br /> <br /> '''tblastn'''- Compares a protein query sequence against a nucleotide database dynamically translated in all reading frames.<br /> <br /> '''tblastx'''- Compares the 6 frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database.</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2891 2006-03-24T19:41:00Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).<br /> <br /> 'insert screen shot here'<br /> <br /> * In the Visualization Area click on the Sequence Alignment tab.<br /> <br /> * Click on the Blast button.<br /> <br /> Note that the result displays the length of the longest sequence selected (here there is only one)due to the sample.<br /> <br /> Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program such as blastn.<br /> <br /> 'insert screen shot here'<br /> <br /> There are five different types of queries you can run, depending on what data you are using:</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2890 2006-03-24T18:02:47Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence &quot;NP_077744-Wilms.fasta&quot;. <br /> <br /> Provide a little background info about Wilm's tumor. (It was chosen at random).</div>

Ginhoven http://wiki.c2b2.columbia.edu/workbench/index.php?title=User:Ginhoven&diff=2889 2006-03-24T16:45:21Z

<p>Ginhoven: </p> <hr /> <div>==TUTORIAL - BLAST==<br /> <br /> In this Tutorial you will learn to:<br /> <br /> * Set up and perform a Blast search.<br /> <br /> * Decipher the Output.<br /> <br /> * Analyze the results.<br /> <br /> <br /> ----<br /> '''OVERVIEW'''<br /> <br /> A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.<br /> <br /> <br /> BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.<br /> <br /> A BLAST search has four components:<br /> <br /> * Query<br /> <br /> * Data Base Program<br /> <br /> * Search Purpose<br /> <br /> * Goal<br /> <br /> <br /> For the purpose of this tutorial use the file &quot;NM _024426-Wilms.Fasta&quot; provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file</div>

Ginhoven