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Nucleic Acids Res. Jan 1, 1998; 26(1): 320–322.
PMCID: PMC147209

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

Abstract

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 http://www.sanger.ac.uk/Pfam/ 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.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Sonnhammer EL, Durbin R. A workbench for large-scale sequence homology analysis. Comput Appl Biosci. 1994 Jun;10(3):301–307. [PubMed]
  • Sonnhammer EL, Kahn D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 1994 Mar;3(3):482–492. [PMC free article] [PubMed]
  • Attwood TK, Beck ME, Bleasby AJ, Degtyarenko K, Michie AD, Parry-Smith DJ. Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res. 1997 Jan 1;25(1):212–217. [PMC free article] [PubMed]
  • Bairoch A, Bucher P, Hofmann K. The PROSITE database, its status in 1997. Nucleic Acids Res. 1997 Jan 1;25(1):217–221. [PMC free article] [PubMed]
  • Henikoff S, Pietrokovski S, Henikoff JG. Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Res. 1998 Jan 1;26(1):309–312. [PMC free article] [PubMed]
  • Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997 Jul;28(3):405–420. [PubMed]
  • Krogh A, Brown M, Mian IS, Sjölander K, Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 1994 Feb 4;235(5):1501–1531. [PubMed]
  • Eddy SR. Hidden Markov models. Curr Opin Struct Biol. 1996 Jun;6(3):361–365. [PubMed]
  • Henikoff S, Endow SA, Greene EA. Connecting protein family resources using the proWeb network. Trends Biochem Sci. 1996 Nov;21(11):444–445. [PubMed]
  • Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998 Jan 1;26(1):38–42. [PMC free article] [PubMed]

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