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Question: Turn Off Blast Search On Reverse Complement Strand In Blastn
7
gravatar for Zhaorong
10.9 years ago by
Zhaorong • 1.3k
State College, PA
Zhaorong • 1.3k wrote:

I have a quick question: How can I turn off search on reverse complement strand of my query nucleotide sequence in blastn?

For example, I don't want 'GUAAAGCCAAAUCUUCGGUUA' to be a hit when I use 'UAACCGAAGAUUUGGCUUUAC' as the query.

Maybe I missed it when I read the man page, but I really appreciate it if someone can point out the parameter I should use.

Thanks!
sequence blast • 56k views
ADD COMMENT • link •
modified 5 months ago by yasopi9568 • 0 • written 10.9 years ago by Zhaorong • 1.3k

I think you should someone take care of the target or subject strandedness as well. You should post - filter the results based on the alignment location I guess in query and subject/ target

ADD REPLY • link written 5 months ago by jayeshkumarsundaram • 0
4
gravatar for Istvan Albert
10.9 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

The -S flag can select the strands:

-S  Query strands to search against database 
    (for blast[nx], and tblastx) 3 is both, 1 is top, 2 is bottom [Integer]
ADD COMMENT • link modified 17 months ago by _r_am ♦ 32k • written 10.9 years ago by Istvan Albert ♦♦ 86k
4

In NCBI BLAST+ this is controlled by the '-strand' option.

ADD REPLY • link written 8.9 years ago by Hamish • 3.2k
2
gravatar for kevin.l.neff
8.6 years ago by
kevin.l.neff • 280
Mayo Clinic College of Medicine
kevin.l.neff • 280 wrote:

For BLAST+, it's -strand {both,plus,minus}
ADD COMMENT • link written 8.6 years ago by kevin.l.neff • 280

I'm not sure this option even works because it's giving me identical results for plus and minus.

ADD REPLY • link written 8.6 years ago by kevin.l.neff • 280
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