Pfam: multiple sequence alignments and HMM-profiles of protein domains

Nucleic Acids Res. 1998 Jan 1;26(1):320-2. doi: 10.1093/nar/26.1.320.


Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members and alignment is done semi-automatically based on expert knowledge, sequence similarity, other protein family databases and the ability of HMM-profiles to correctly identify and align the members. Release 2.0 of Pfam contains 527 manually verified families which are available for browsing and on-line searching via the World Wide Web in the UK at and in the US at http://genome.wustl. edu/Pfam/ Pfam 2.0 matches one or more domains in 50% of Swissprot-34 sequences, and 25% of a large sample of predicted proteins from the Caenorhabditis elegans genome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Caenorhabditis elegans
  • Computer Communication Networks
  • Databases, Factual*
  • Information Storage and Retrieval
  • Markov Chains
  • Models, Molecular
  • Molecular Sequence Data
  • Proteins / chemistry*
  • Sequence Alignment*


  • Proteins