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BLAST - Exclude complement sequences (Read 6620 times)
Oct 28th, 2013 at 3:51pm

Tim Cooper   Offline
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Hi  Smiley

I am running BLAST searches against a custom DB - I was wondering if there was a way to remove complement hits from the annotations list and/or export to FASTA only the non-complement hits. Thanks!

- TJC
 
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Reply #1 - Nov 4th, 2013 at 8:45pm

Konstantin Okonechnikov   Offline
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Hi Tim,

thanks for your report!

The strand option is missing from BLAST interface, but it will be added in the next minor release:
https://ugene.unipro.ru/tracker/browse/UGENE-2396

Unfortunately I am not aware of an easy way to filter annotations by strand. This could be a good improvement for future versions. However one possible option is to sort the annotations by "strand" and then export only those which have direct strand.

First, select one of the blast_result annotations in the Annotation Editor and right-click the qualifier called "source_frame". From the conext menu select option Add 'source_frame' column (Screenshot 1)

An additional column will appear in the Annotations Editor. Clicking on this column will sort the annotations based on the valuse of the corresponding qualifer: direct or complmenet

Now it is possible to easy select only those annotations which have complement strand (using selection with Shift key) and remove them. (Screenshot 2)

Let me know, if this worked for you.
 

screenshot_01.png (119 KB | )
screenshot_01.png
screenshot_02.png (141 KB | )
screenshot_02.png
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Reply #2 - Nov 7th, 2013 at 4:38pm

Tim Cooper   Offline
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Thanks Smiley That is exactly what I needed.

- TJC
 
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