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BLAST CDS from annotated genome file (Read 127 times)
Jul 13th, 2018 at 10:43am

felince tokyo   Offline
YaBB Newbies

Posts: 1

Maybe this is a very basic question but I really don't know how UGENE handles BLAST of a complete annotated bacterial genome sequence against a amino acid database. I want to BLAST my genome but only the annotated CDS so when I search the amino acid database, the results are annotated on the genome as annotations overlapping the CDS. What I'm obtaining are hits annotated on intergenic regions as well. How do I restrict BLAST search to only the annotated CDS of the entire sequence?

Thank you in advance  Smiley.

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Reply #1 - Jul 13th, 2018 at 2:41pm

Olga Golosova   Offline
YaBB Administrator

Posts: 237
Hi Felipe!

I didn't get which BLAST you use as we have NCBI BLAST, local BLAST and BLAST+. However, I see two approaches in general:
1) Do BLAST for the whole sequence, then filter out annotations that do not intersect the CDS annotations.
2) Extract the CDS regions and then do BLAST for them.

For the first approach you may try to use the "Intersect annotations" sample workflow. Feel free to ask additional questions, if you need help with that.

You're welcome! Smiley
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