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?

  • $\begingroup$ 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

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.


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