Force BlastN to align only to minus strand of subject

Question

[mwittep]

Hi! I'm trying to blast a sequence where I have a TSS signal (e.g. using CapSeq) that comes from the minus strand, against a chosen genome. I already have the reverse compliment of the sequence i.e. the reverse compliment of the position of the genome, so I'm trying to force BLASTN to only use the minus strand of the chosen subject. Sadly I only found the command -strand, which takes the rev. compliment of the query and not the subject.

Did I miss the parameter in the documentation or how do you do this?

Thanks in advance!

Answer 1

[Qiongyi]

After blastn, you can only look at the Plus/Minus strand results (that is your query vs. the reverse complement of the subject). Alternatively, you can do reverse complement for your subject sequence first, and then blastn and choose only the plus/plus strand results. You can use the default setting ("-strand both") or "-strand plus". It doesn't really matter in terms of the running speed using a local blast, I think.