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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