Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

Authors: Bateman, Alex; Birney, Ewan; Durbin, Richard; Eddy, Sean R.¹; Finn, Robert D.; Sonnhammer, Erik L. L.²

Source: Nucleic Acids Research, Volume 27, Number 1, 01 January 1999 , pp. 260-262(3)

Publisher: Oxford University Press

Buy & download fulltext article:

The full text is free.

View now:

PDF

Abstract:

Pfam is a collection of multiple alignments and profile hidden Markov models of protein domain families. Release 3.1 is a major update of the Pfam database and contains 1313 families which are available on the World Wide Web in Europe at http://www.sanger.ac.uk/Software/Pfam/ and http://www.cgr.ki.se/Pfam/ , and in the US at http://pfam.wustl.edu/ . Over 54% of proteins in SWISS-PROT-35 and SP-TrEMBL-5 match a Pfam family. The primary changes of Pfam since release 2.1 are that we now use the more advanced version 2 of the HMMER software, which is more sensitive and provides expectation values for matches, and that it now includes proteins from both SP-TrEMBL and SWISS-PROT.

Document Type: Research article

Affiliations: 1: Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA and 2: Center for Genomics Research, Karolinska Institutet, S-171 77 Stockholm, Sweden

Publication date: 1999-01-01

More about this publication?

Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.