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?

$\endgroup$
  • $\begingroup$ 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 '15 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 '15 at 16:24
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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.