Low Stringency Blast (To Find Outgroups)

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10.5 years ago

vilsnk ▴ 30

Hi!

I'm looking for a way to find appropriate outgroup sequences for my paralog phylogenetic tree. Is there a way, using blast, that I can find sequences that are only a little similar to my query sequence? Currently I have the problem that any gene I try from blast (even those with very high E values) turns out to be closely related to one of my family members. When I try to expand my number of hits I usually exceed the CPU time allocated. Is there an established way using blast or some other program (given a nucleotide sequence) to find fairly low similarity matches?

I am currently using my genes' NT sequences and attempting a tblastx search.

Thanks in advance.

phylogenetics blast • 3.0k views

ADD COMMENT • link 10.5 years ago by vilsnk ▴ 30

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Try psi-blast with a lot of iterations.

ADD REPLY • link 10.5 years ago by Damian Kao 16k

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Thanks, I'll do that.

ADD REPLY • link 10.5 years ago by vilsnk ▴ 30

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