UNIT 2.5 Identifying Protein Domains with the Pfam Database

  1. Robert Finn,
  2. Sam Griffiths-Jones,
  3. Alex Bateman

Published Online: 1 MAY 2003

DOI: 10.1002/0471250953.bi0205s01

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Finn, R., Griffiths-Jones, S. and Bateman, A. 2003. Identifying Protein Domains with the Pfam Database. Current Protocols in Bioinformatics. 1:2.5:2.5.1–2.5.19.

Author Information

  1. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, United Kingdom

Publication History

  1. Published Online: 1 MAY 2003
  2. Published Print: MAR 2003

This is not the most recent version of the article. View current version (1 SEP 2008)


Pfam is a database of such protein domain families, with each family represented by multiple sequence alignments and profile hidden Markov models (HMMs). In addition, each family has associated annotation, literature references and links to other databases. The entries in Pfam are available via the worldwide web and in flatfile format. This unit contains detailed information on how to access and utilise the information present in the Pfam database, namely the families, multiple alignments and annotation. Details on running Pfam, both remotely and locally are presented.