Lab: Using hmmer

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• What's HMMER
  
  New to hmmer3
  1. phmmer: The phmmer program is for searching a single sequence query against a sequence database (BLASTP-like). phmmer works essentially just like hmmsearch does, except you provide a query sequence instead of a query profile HMM. Internally, HMMER builds a profile HMM from your single query sequence, using a simple position-independent scoring system (BLOSUM62 scores converted to probabilities, plus a gap-open and gap-extend probability).
  2. jackphmmer: Iteratively search a sequence against a sequence database (PSIBLAST-like).
  3. "Sequence scores, not alignment scores. Alignment uncertainty has an important impact on the power of sequence database searches. It’s precisely the most remote homologs – the most difficult to identify and potentially most interesting sequences – where alignment uncertainty is greatest, and where the statistical approximation inherent in scoring just a single best alignment breaks down the most. To maximize power to discriminate true homologs from nonhomologs in a database search, statistical inference theory says you ought to be scoring sequences by integrating over alignment uncertainty, not just scoring the single best alignment. HMMER3’s log-odds scores are sequence scores, not just optimal alignment scores; they are integrated over the posterior alignment ensemble." (quote from HMMER user's guide)
  4. MSV filter. The main acceleration heuristic used in HMMER3. The MSV (“Multiple Segment Viterbi”) algorithm looks for one or more high-scoring ungapped alignments. If the MSV score passes a set threshold, the entire sequence passes on to the next pipeline step; else it is rejected.
• HMMER web server
1. phhmer: Protein sequence vs protein sequence database
2. hmmscan: protein sequence vs profile-HMM database
3. hmmsearch: protein alignment/profile-HMM vs protein sequence database
4. jackhmmer: iterative search (of sequence, HMM, or multiple alignment) vs protein sequence database
• Try it out on bradbury (executables are under /home/yye/BioTools/hmmer-3.0/src on Bradbury; samples files are under tutorial/)
  HMMER user's guide
  1. hmmbuild globins4.hmm tutorial/globins4.sto
  2. hmmsearch globins4.hmm tutorial/globins45.fa > globins4.out
  3. hmmbuild globins4.hmm tutorial/globins4.sto
  4. hmmbuild fn3.hmm tutorial/fn3.sto
  5. hmmbuild Pkinase.hmm tutorial/Pkinase.sto
  6. cat globins4.hmm fn3.hmm Pkinase.hmm > minifam
  7. hmmpress minifam
  8. hmmscan minifam tutorial/7LESS_DROME
  9. phmmer tutorial/HBB_HUMAN tutorial/globins45.fa