Low Stringency Blast (To Find Outgroups)

Question

[vilsnk]

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.

[Damian Kao]

Try psi-blast with a lot of iterations.

[vilsnk]

Thanks, I'll do that.