Difference between revisions of "Pattern Discovery"
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For this tutorial, we will begin with the set of sequences retrieved in the '''Sequence Retriever''' tutorial. These sequences derive from a cluster of genes showing similar expression pattern across a number of different experiments. | For this tutorial, we will begin with the set of sequences retrieved in the '''Sequence Retriever''' tutorial. These sequences derive from a cluster of genes showing similar expression pattern across a number of different experiments. | ||
| − | (Note - there currently is no provision for filtering repeated sequences out from genomic seqeuence. Results should be evaluated in this light). | + | ('''Note''' - there currently is no provision for filtering repeated sequences out from genomic seqeuence. Results should be evaluated in this light). |
==Setting parameters and running== | ==Setting parameters and running== | ||
Revision as of 17:20, 20 March 2006
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Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials |
Analysis Framework | ANOVA | ARACNe | BLAST | Cellular Networks KnowledgeBase | CeRNA/Hermes Query | Classification (KNN, WV) | Color Mosaic | Consensus Clustering | Cytoscape | Cupid | DeMAND | Expression Value Distribution | Fold-Change | Gene Ontology Term Analysis | Gene Ontology Viewer | GenomeSpace | genSpace | Grid Services | GSEA | Hierarchical Clustering | IDEA | Jmol | K-Means Clustering | LINCS Query | Marker Annotations | MarkUs | Master Regulator Analysis | (MRA-FET Method) | (MRA-MARINa Method) | MatrixREDUCE | MINDy | Pattern Discovery | PCA | Promoter Analysis | Pudge | SAM | Sequence Retriever | SkyBase | SkyLine | SOM | SVM | T-Test | Viper Analysis | Volcano Plot |
Contents
Background
The geWorkbench Pattern Discovery module uses an algorithm called SPLASH to search for common patterns in sets of DNA or protein sequences. This type of search can be used, for example, to search for common regulatory elements in otherwise unrelated sequences.
For this tutorial, we will begin with the set of sequences retrieved in the Sequence Retriever tutorial. These sequences derive from a cluster of genes showing similar expression pattern across a number of different experiments.
(Note - there currently is no provision for filtering repeated sequences out from genomic seqeuence. Results should be evaluated in this light).
Setting parameters and running
A number of parameters can be adjusted by the user, as shown in the figure, to adjust the sensitivity of the search. A user name must be entered, but it can be any name.
Push Create to start the search.
Viewing results
The result of the search can be viewed both in the Pattern Discovery module itself and in other sequence viewer modules such as "Sequence" and "Promoter".
Results are added to the Projects Folder
The results of a run of Pattern Discovery are placed in the Project Folder:
