blast strand plus minus
Hi,
I have a doubt wit hthe blast output. So I have blast scaffolds to genes in order to do a multiple alignment.
Should I reversed-complement all my scaffolds that have been assigned to strand:
+ -
- +
- -
(First part is my query, second is the subject)
The idea is to get all the scaffolds to the same direction for multiple alignment.
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I’m not sure I fully understand, but BLAST will let you specify whether you want to retrieve matches that are on the plus, minus, or both strands.