Hidden Markov Model --- search for remote relatives
Unlike Blast, where a single query sequence is used to search a database for
related sequences, hidden Markov Model (HMM) search uses a family of related
sequences as query. A multiple sequence alignment is first built from
the input sequences, and then a mathematical model (HMM) or profile of
the multiple alignment is built. This model or profile will be used to
query a sequence database to find additional family members who are more distant
relatives of the original family.
- HMM is behind the protein domain database Pfam.
- SAM HMM
for remote protein homolog search and secondary structure prediction is available
at UC Santa Cruz.
- A stand-only version of HMM program HMMER 2.2
can be down loaded from http://hmmer.wustl.edu/.