Pfam

Pfam is a database that contains a collection of protein families that are defined by multiple sequence alignments using Hidden Markov Models. Pfam groups related entries into clans by the similarity of sequence, structure, or profile-HMM. The data for each entry is based on the UniProt Reference Proteomes.

Topic

Proteins;Gene and protein families;Data management;Protein folds and structural domains;Sequence sites, features and motifs;Sequence composition, complexity and repeats;Sequence analysis

Detail

  • Operation: Data retrieval;Query and retrieval;Sequence feature detection;Protein feature detection

  • Software interface: Web API;Web application;Database portal

  • Language: -

  • License: CC0

  • Cost: Free

  • Version name: 35.0

  • Credit: The Sangerthe Wellcome Trust. the MRC, the National Institutes of Health National Center for Human Genome Research.

  • Input: any type of accession, ID, or keyword(s)

  • Output: -

  • Contact: pfam-help@ebi.ac.uk

  • Collection: -

  • Maturity: Mature

Publications

  • Pfam 10 years on: 10,000 families and still growing
  • Sammut SJ, Finn RD, Bateman A. Pfam 10 years on: 10,000 families and still growing. Brief Bioinform. 2008 May;9(3):210-9.
  • https://doi.org/10.1093/bib/bbn010
  • PMID: 18344544
  • PMC: -
  • Pfam: multiple sequence alignments and HMM-profiles of protein domains
  • Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 1998 Jan 1;26(1):320-2.
  • https://doi.org/10.1093/nar/26.1.320
  • PMID: 9399864
  • PMC: PMC147209
  • Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
  • Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 1999 Jan 1;27(1):260-2.
  • https://doi.org/10.1093/nar/27.1.260
  • PMID: 9847196
  • PMC: PMC148151

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