Lab: Using hmmer
- What's HMMER
New to hmmer3
- 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).
- jackphmmer: Iteratively search a sequence against a sequence database (PSIBLAST-like).
- "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)
- 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
- phhmer: Protein sequence vs protein sequence database
- hmmscan: protein sequence vs profile-HMM database
- hmmsearch: protein alignment/profile-HMM vs protein sequence database
- 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
- hmmbuild globins4.hmm tutorial/globins4.sto
- hmmsearch globins4.hmm tutorial/globins45.fa > globins4.out
- hmmbuild globins4.hmm tutorial/globins4.sto
- hmmbuild fn3.hmm tutorial/fn3.sto
- hmmbuild Pkinase.hmm tutorial/Pkinase.sto
- cat globins4.hmm fn3.hmm Pkinase.hmm > minifam
- hmmpress minifam
- hmmscan minifam tutorial/7LESS_DROME
- phmmer tutorial/HBB_HUMAN tutorial/globins45.fa