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Ugene Query Designer (Read 4807 times)
Jan 19th, 2011 at 7:05pm

Petr Golubev   Offline
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Since version 1.9.0 a new sequence analyze tool "Query Designer" is available in UGENE. This tool allows you to find sequence regions containing specified set of features.

For instance, you can search a sequence for open reading frames surrounded by repeat units using supplied sample query file as follows (post below contains pictures):

1. Open a sequence in the Sequence view.
2. Activate the context menu and select 'Analyze -> Analyze with query schema'. Pic.1
3. In the 'File with query' field select '$UGENE/data/query_samples/RepeatsWithORF.uql'. Pic.2
4. Click 'Search'.
5. Obtained annotations are collected in groups so that every group contains an ORF surrounded by repeat pair units. Pic.3

Any feedback is welcome.
« Last Edit: Jan 20th, 2011 at 1:27pm by Konstantin Okonechnikov »  
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Reply #1 - Jan 19th, 2011 at 7:06pm

Petr Golubev   Offline
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Documentation on creating and editing query file using GUI interface or text editor is available at:
http://ugene.unipro.ru/documentation/qd_manual/index.html
 

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