Difference between revisions of "Pattern Discovery"
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| + | __TOC__ | ||
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| + | ==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. | ||
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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. | ||
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| + | ==Setting parameters and running== | ||
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| + | 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. | ||
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| + | Push '''Create''' to start the search. | ||
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| + | [[Image:T_PatternDiscovery_Run.png]] | ||
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| + | ==Viewing results== | ||
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| + | 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". | ||
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| + | [[Image:T_PatternDiscovery_Result.png]] | ||
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| + | ==Results are added to the Projects Folder== | ||
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| + | The results of a run of '''Pattern Discovery''' are placed in the Project Folder: | ||
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| + | [[Image:T_ProjectFolder_PatternDiscovery.png]] | ||
Revision as of 02:59, 28 February 2006
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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.
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:
