Question: Low Stringency Blast (To Find Outgroups)
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gravatar for vilsnk
6.9 years ago by
vilsnk30
vilsnk30 wrote:

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 • 2.1k views
ADD COMMENTlink written 6.9 years ago by vilsnk30
1

Try psi-blast with a lot of iterations.

ADD REPLYlink written 6.9 years ago by Damian Kao15k

Thanks, I'll do that.

ADD REPLYlink written 6.9 years ago by vilsnk30
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