blast strand plus minus

Question

[Picasa]

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.

[Joe]

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.