7
$\begingroup$

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss.

I am only looking at a small (20AA) sequence and it is helical throughout.

Is hhpred still likely to pick up on subtle similarities in the basic secondary structure as it would in a folded protein sequence, or would simpler alignment be just as appropriate?

$\endgroup$
2
  • $\begingroup$ Hi there - seems like you may get an answer from someone on BioStars or another site with more computational/statistical expertise - as this question is not really biological per se, more bioinformatic $\endgroup$
    – Luke
    Mar 23, 2015 at 11:01
  • $\begingroup$ Thanks for the tip, I'll give that a go. I think this question is right at the fringe of what is appropriate for this site, but you never know! Someone might have come across this problem before! $\endgroup$
    – James
    Apr 21, 2015 at 16:24

1 Answer 1

1
$\begingroup$

TMHMM is a very good standard on predicting the TMHs in the first place, so it stands to reason that predicting homologues using this approach is completely viable.

$\endgroup$

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .