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PMID: 9399864 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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

Nucleic acids research ·Vol. 26 ·No. 1 ·1998-01-01 ·Pages 320-2

Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R

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.

MeSH Terms
Amino Acid Sequence Animals Caenorhabditis elegans Computer Communication Networks Databases, Factual Information Storage and Retrieval Markov Chains Models, Molecular Molecular Sequence Data Proteins/chemistry Sequence Alignment
Chemicals
Proteins
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Sonnhammer E L
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Building 38A, Room 8N805, National Institutes of Health, Bethesda, MD 20894, USA. [email protected]
Eddy S R
Birney E
Bateman A
Durbin R
References (10)
10 references, click to expand
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/26.1.320
Email
[email protected]
Published
1998-01-01
Pages
320-2
Language
English
Region
England
NLM ID
0411011
PMCID
PMC147209
Subset
IM
Grants
NHGRI NIH HHS · R01-HG01363 · United States
Wellcome Trust · United Kingdom
External Links
PubMed source DOI: 10.1093/nar/26.1.320 PMC Full Text View journal details
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