Sequence Retriever - Revision history

Smith: /* Using the Sequence Retriever */

2014-04-22T19:14:16Z

‎Using the Sequence Retriever

Smith at 18:29, 23 January 2014

2014-01-23T18:29:32Z

Smith: /* Saving Sequences to the Project */

2014-01-23T18:27:13Z

‎Saving Sequences to the Project

Smith: /* DNA Sequences */

2014-01-23T18:19:50Z

‎DNA Sequences

Smith: /* Protein Sequences */

2014-01-23T18:13:28Z

‎Protein Sequences

Smith: /* DNA Sequences */

2014-01-23T18:12:18Z

‎DNA Sequences

Smith: /* Controls */

2014-01-23T18:10:37Z

‎Controls

Smith: /* DNA Sequences */

2014-01-23T17:54:33Z

‎DNA Sequences

Smith: /* Prerequisites */

2014-01-23T17:37:32Z

‎Prerequisites

Smith: /* Overview */

2014-01-23T17:31:41Z

‎Overview

@@ Line 62: / Line 62: @@
 Once sequences have been retrieved, some or all can be added to the [[Workspace]] as a new data node ("Add to Workspace" button).
-'''Note''' - retrieved sequences are not guaranteed to be retained if the marker set using in the query is deactivated, or if the user selects a different data node in the Workspace and then returns to the previous node.  One can switch back and forth between DNA and Protein query results within the context of the same marker set.
+'''Note''' - retrieved sequences are not guaranteed to be retained if the marker set using in the query is deactivated, or if the user selects a different data node in the [[Workspace]] and then returns to the previous node.  One can switch back and forth between DNA and Protein query results within the context of the same marker set.
 ===Prerequisites===

@@ Line 12: / Line 12: @@
 For DNA queries, the RefSeq gene(s) associated with a given probeset are obtained from the annotation file and used for the query.  For protein queries, UniProt IDs from the annotation file are used.  If multiple IDs are present for a marker, they are all used.
-One the desired sequences have been downloaded, they can be viewed or saved to the Project Folders component for use by other components. Examples include running [[BLAST|BLAST]] searches, looking for the presence of known promoter motifs ([[Promoter_Analysis | Promoter Analysis]]), or looking for patterns in a set of sequences using [[Pattern_Discovery|Pattern Discovery]].
+One the desired sequences have been downloaded, they can be viewed or saved to the [[Workspace]] for use by other components. Examples include running [[BLAST|BLAST]] searches, looking for the presence of known promoter motifs ([[Promoter_Analysis | Promoter Analysis]]), or looking for patterns in a set of sequences using [[Pattern_Discovery|Pattern Discovery]].
 ==Controls==
@@ Line 31: / Line 31: @@
 * '''Get Sequence''' - Launches the query using the selected markers.
-* '''Add to Project''' - Add selected sequences returned by the query to the Project Folders component.
+* '''Add to Workspace''' - Add selected sequences returned by the query to the [[Workspace]].
 * '''View''' - Line or Full Sequence.
@@ Line 37: / Line 37: @@
 * '''Show only unique transcript-start sites''' - Applies to DNA queries only.  When checked, only a single sequence entry for a given transcript start site will be shown.  If the box is unchecked, all RefSeq sequences associated with the probeset in the annotation file, and for which sequences were retrieved, will be shown.
-* '''Include''' - Check boxes for sequences to copy to the Project Folders component when "Add to Project" is pushed.
+* '''Include''' - Check boxes for sequences to copy to the [[Workspace]] when "Add to Workspace" is pushed.
 * '''Name'''  -  The name for a sequence is formed by concatenating the marker name with the chromosome number of physical location of the sequence on the chromosome, e.g. in 35694_at_chr2_102314487, "35694_at" is the probeset id, and the sequence is located on chromosome 2 at position 102314487.
@@ Line 60: / Line 60: @@
 For DNA sequences, the Sequence Retriever retrieves genomic sequence from the Golden Path database at the UC Santa Cruz.  The amount of sequence upstream and downstream to fetch can be specified in the range settings (-+).
-Once sequences have been retrieved, some or all can be added to the Project Folders component as a new data node (Add to Project button).
+Once sequences have been retrieved, some or all can be added to the [[Workspace]] as a new data node ("Add to Workspace" button).
 '''Note''' - retrieved sequences are not guaranteed to be retained if the marker set using in the query is deactivated, or if the user selects a different data node in the Workspace and then returns to the previous node.  One can switch back and forth between DNA and Protein query results within the context of the same marker set.
@@ Line 197: / Line 197: @@
 ==Saving sequences to an external FASTA file==
-Once a group of sequences has been saved to the Project Folders component, they can also be saved to a file on disk.
+Once a group of sequences has been saved to the [[Workspace]], they can also be saved to a file on disk.
-# Right-click on the sequence node in the Project Folders component.
+# Right-click on the sequence node in the [[Workspace]].
 # Select Save.
 # Enter a suitable name and save the file.

@@ Line 179: / Line 179: @@
 [[Image:Sequence_Retriever_DNA_Full__Sequence_View.png]]
-===Saving Sequences to the Project===
+===Saving Sequences to the Workspace===
-To the left of each retrieved sequence is a check-box, in the column titled "Include".  To save sequences to the Project Folders component, select those desired by checking the adjacent boxes, and then press "Save to Project".
+To the left of each retrieved sequence is a check-box, in the column titled "Include".  To save sequences to the [[Workspace]], select those desired by checking the adjacent boxes, and then press "Save to Workspace".
@@ Line 187: / Line 187: @@
-All sequences saved at one time will appear in a single new node in the Project Folders component.  You will be prompted to enter a name for the new data sequence node.  Here we have given the node the name "MAP4K4_seqs".
+All sequences saved at one time will appear in a single new node in the [[Workspace]].  You will be prompted to enter a name for the new data sequence node.  Here we have given the node the name "MAP4K4_seqs".
-[[Image:Project_Folders_MAP4K4_2_seqs.png]]
+[[Image:Sequence_Retriever_seqs_in_Workspace.png]]
-Note that when this node is selected, the Viewing area of the geWorkbench GUI will now show components that support working with sequences.  However, the Sequence Retrieval component will no longer be visible!  You must select the Project or the sequence's parent object to see the Sequence Retrieval component again.
+Note that when this node is selected, the Viewing area of the geWorkbench GUI will now show components that support working with sequences.  However, the Sequence Retrieval component will no longer be visible!  You must select the  sequence's parent object to see the Sequence Retrieval component again.
 ==Saving sequences to an external FASTA file==

← Older revision		Revision as of 18:19, 23 January 2014
Line 105:		Line 105:

	'''Note''' - If sequences are retrieved for multiple markers, selecting a marker in the list will cause only its hits to be displayed. If no markers are selected in the list, hits for all markers will be displayed.		'''Note''' - If sequences are retrieved for multiple markers, selecting a marker in the list will cause only its hits to be displayed. If no markers are selected in the list, hits for all markers will be displayed.
		+
		+	Clicking on a particular sequence under Sequence Detail will display its actual sequence in the scrolling box below.

@@ Line 122: / Line 122: @@
 ====Protein Sequences====
 '''Protein Sequence Naming''' - For protein results, the sequence name is formed by concatenating the probeset id with the UniProt ID of the sequence.
@@ Line 131: / Line 127: @@
 '''Note''' - If sequences are retrieved for multiple markers, selecting a marker in the list will cause only its hits to be displayed.  If no markers are selected in the list, hits for all markers will be displayed.

@@ Line 100: / Line 100: @@
 ====DNA Sequences====
 '''DNA Sequence Naming''' - Each retrieved sequence is given a name formed by concatenating the probeset name for the marker, the refSeq identifier, the chromosome, and the location on the chromosome of the transcript start site obtained from the UCSC refGene table.
@@ Line 112: / Line 109: @@
 [[Image:Sequence_Retriever_MAP_DNA_results.png|{{ImageMaxWidth}}]]
-Selecting just the marker for MAP4K4 in the marker list restricts the display to its hits.
+Selecting just the marker for MAP4K4 in the marker list restricts the display to its hits.  For the MAP4K4 marker, genomic sequence for two unique transcript start sites was retrieved.

← Older revision		Revision as of 18:10, 23 January 2014
Line 48:		Line 48:


−	[[Image:~~Sequence_Retriever_MAP4K4_DNA_result~~.png\|{{ImageMaxWidth}}]]	+	[[Image:Sequence_Retriever_MAP_DNA_results.png\|{{ImageMaxWidth}}]]

	==Using the Sequence Retriever==		==Using the Sequence Retriever==

← Older revision		Revision as of 17:54, 23 January 2014
Line 118:		Line 118:


−	Unchecking the "Show only unique transcript-start sites" box adds ~~one~~ additional ~~result. It has the same transcript start site, but a~~ different RefSeq ID.	+	Unchecking the "Show only unique transcript-start sites" box adds additional sequences with different RefSeq IDs.

← Older revision		Revision as of 17:37, 23 January 2014
Line 82:		Line 82:


−	[[Image:Sequence_Retriever_Initial_State.png~~\|{{ImageMaxWidth}}~~]]	+	[[Image:Sequence_Retriever_Initial_State.png]]

	===Retrieving Sequences===		===Retrieving Sequences===

@@ Line 6: / Line 6: @@
 The Sequence Retriever component fetches the DNA or protein sequences for selected gene markers from remote databases.  Nucleotide sequences are retrieved from the GoldenPath database hosted at the UC Santa Cruz.  Amino-acid sequences are retrieved from the European Bioinformatics Institute (EBI).
-DNA sequences are retrieved using the transcript start site obtained for the desired gene from the refGenes table at UCSC. This table lists refSeq genes available for each supported species.  (Prior to geWorkbench release 2.2.1, the KnownGenes table was used, which supported only human, mouse and rat).
+DNA sequences are retrieved using the transcript start site obtained for the desired gene from the refGenes table at UCSC. This table lists refSeq genes available for each supported species.
 The Sequence Retriever component functions only in the context of microarray datasets. The component also depends on the microarray platform annotation file, which must be loaded when the microarray dataset is read into geWorkbench.