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Restriction enzyme searching, annotation (Read 6683 times)
Jun 18th, 2010 at 4:09am

JohnR   Offline
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I would like to be able to search for restriction enzymes by category of restriction site - for example to select all enzymes with 6 bp or 4 bp recognition sites. A feature like this is incorporated in WebCutter (http://rna.lundberg.gu.se/cutter2/).

Also, when doing a restriction enzyme search, the sites were annotated on the circular map, which is very helpful. However, when I did a new search, the annotations from the second search were added to the first. This gets cluttered pretty quickly. Is there a way to either delete the annotations on the map or have annotations from a new search replace the old ones.

Thanks for the great program!

JohnR
 
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Reply #1 - Jun 29th, 2010 at 4:16pm

Oleg Godovykh   Offline
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Hi John!
Concerning the first feature you have requested: we put it on our TODO-list and hope to implement in 1.7.1 release.  UGENE has filtering by number of results option in the current version, so we have to add only filtering by length of recognition sites, similar to Webcutter.
 
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Reply #2 - Jun 29th, 2010 at 4:16pm

Oleg Godovykh   Offline
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In order to keep your annotations "grouped" by different search requests, you can use group names in Restriction Enzymes dialog.

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By default, the group name is set to <auto>, and all annotations are stored in the "enzyme" group.

If you set different group names for different searches, you will be able to delete results of search from the context menu for group in main window:

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Thanks for your interest in UGENE!
 
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