The Pfam Protein Families Database

Abstract

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.

Keywords

BiologyUniProtComputational biologyAnnotationSequence alignmentProtein domainProtein familyBioinformaticsGeneticsPeptide sequenceGene

Affiliated Institutions

Wellcome Sanger Institute GB

Related Publications

ROBERT FINN , John Tate , Jaina Mistry +8 more

Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam ...

2007 Nucleic Acids Research 1831 citations

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

Brigitte Boeckmann , Amos Bairoch , Rolf Apweiler +9 more

The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Scie...

2003 Nucleic Acids Research 3907 citations

The Pfam protein families database in 2019

Sara El-Gebali , Jaina Mistry , Alex Bateman +13 more

This FAIRsharing record describes: The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)....

2018 Nucleic Acids Research 4869 citations

Rfam 11.0: 10 years of RNA families

Sarah Burge , Jennifer Daub , Ruth Y. Eberhardt +6 more

The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily...

2012 Nucleic Acids Research 832 citations

Generating consensus sequences from partialorder multiple sequence alignment graphs

Christopher J. Lee

Abstract Motivation: Consensus sequence generation is important in many kinds of sequence analysis ranging from sequence assembly to profile-based iterative search methods. Howe...

2003 Bioinformatics 99 citations

Publication Info

Year: 2002
Type: article
Volume: 30
Issue: 1
Pages: 276-280
Citations: 14207
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

The Pfam Protein Families Database

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

14207

OpenAlex

Cite This

APA Style

                            
                                
                                    Alex Bateman, 
                                
                                    Ewan Birney, 
                                
                                    Lorenzo Cerruti
                                
                                et al.
                            
                            (2002). 
                            The Pfam Protein Families Database. 
                            Nucleic Acids Research
                            , 30
                            (1)
                            , 276-280.
                            https://doi.org/10.1093/nar/30.1.276
                        

Identifiers

DOI: 10.1093/nar/30.1.276