Pfam

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Pfam ( P rotein Fam ilies) is a freely accessible database for bioinformatics purposes. On the one hand, there is a machine categorization of protein domains that includes all known proteins . The basis is pattern recognition using machine learning of the amino acid sequence . On the other hand, the patterns determined in this way can be found again in new proteins, which gives an indication of the composition of these proteins from domains and thus also of their function or, in the case of enzymes , of the enzymatic activity . Pfam provides a web service for this forecast.

Pfam consists of two parts, Pfam-A and Pfam-B. Well characterized domains are combined in Pfam-A, while domains with an unknown function are in Pfam-B. The method of machine clustering and pattern recognition are hidden Markov models .

Pfam was established in 1997 by bioinformaticians Erik Sonnhammer ( Karolinska Institutet near Stockholm), Sean Eddy ( Washington University in St. Louis , USA), and Richard Durbin ( Wellcome Trust Sanger Institute near Cambridge, UK). Update 18 was released in early 2006 with a number of additional functions . Pfam 27.0 was released in March 2013.

literature

  1. ^ R. Durbin, S. Eddy, A. Krogh, G. Mitchison: Biological Seqeuence Analysis . Cambridge University Press, Cambridge 1998, ISBN 0-521-62041-4 .
  2. ↑ EL Sonnhammer, SR Eddy, R. Durbin: Pfam: a comprehensive database of protein domain families based on seed alignments. In: Proteins. 28, 1997, pp. 405-420. PMID 9223186
  3. ↑ RD Finn, J. Mistry, B. Schuster-Bockler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, SR Eddy, EL Sonnhammer, A. Bateman: Pfam: clans, web tools and services. In: Nucleic Acids Res. 34, 2006, pp. D247-D251. PMID 16381856
  4. ↑ pfam.sanger.ac.uk: Pfam 27.0 (Mar 2013, 14831 families) ( Memento of the original from February 17, 2010 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. @1@ 2Template: Webachiv / IABot / pfam.sanger.ac.uk

Web links

Access to Pfam: