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How BLAST - (Feb/15/2011 )

Hello everyone,
I do not know if this is right category. I am a beginner in molecular biology. Someone could explain me how to BLAST sequences of DNA forward and reverse? I do the reverse complement of the reverse sequence and then aligned with the forward?

thanks for the advice



You don't need to worry about the complementary strand, the BLAST program automatically takes care of that, ie, if the complementary sequence of your query sequence has hits, BLAST will return the results.


to specify the strand in the blast program use the -S param

-S N (bl2seq, blast2, blastall, blastall_old, blastcl3,
megablast) Query strands to search against database for blastn,
blastx, tblastx:
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3 both (default)