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Star Republic: Guide for Biologists

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