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The Pfam protein families database.

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (, the USA ( and Sweden (

Pubmed ID: 19920124


  • Finn RD
  • Mistry J
  • Tate J
  • Coggill P
  • Heger A
  • Pollington JE
  • Gavin OL
  • Gunasekaran P
  • Ceric G
  • Forslund K
  • Holm L
  • Sonnhammer EL
  • Eddy SR
  • Bateman A


Nucleic acids research

Publication Data

January 22, 2010

Associated Grants

  • Agency: Wellcome Trust, Id: 087656
  • Agency: Biotechnology and Biological Sciences Research Council, Id: BB/F010435/1
  • Agency: Medical Research Council, Id: MC_U137761446
  • Agency: Wellcome Trust, Id: WT077044/Z/05/Z
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Amino Acid Sequence
  • Animals
  • Computational Biology
  • Databases, Nucleic Acid
  • Databases, Protein
  • Genome, Archaeal
  • Genome, Fungal
  • Humans
  • Information Storage and Retrieval
  • Internet
  • Molecular Sequence Data
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Software