databases > DOI:10.25504/FAIRsharing.y3scf6
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General Information
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.


This record replaces or incorporates the following deprecated resources:

Homepage http://pfam.xfam.org/

Countries that developed this resource Austria , Belgium , Croatia , Czech Republic , Denmark , Finland , France , Germany , Greece , Hungary , Iceland , Israel , Italy , Lithuania , Luxembourg , Malta , Montenegro , Netherlands , Norway , Portugal , Republic of Ireland , Slovakia , Spain , Sweden , Switzerland , United Kingdom , United States

Created in 1996

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Subjects 



In the following recommendations:




How to cite this record FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 23, 2021, 3:52 p.m.; Last accessed: Nov 27 2021 11:19 p.m.

Publication for citation  The Pfam protein families database in 2019. El-Gebali S,Mistry J,Bateman A,Eddy SR,Luciani A,Potter SC,Qureshi M,Richardson LJ,Salazar GA,Smart A,Sonnhammer ELL,Hirsh L,Paladin L,Piovesan D,Tosatto SCE,Finn RD; Nucleic Acids Res ; 2018; 10.1093/nar/gky995;


This record is maintained by agb@ebi.ac.uk

Record updated: Feb. 23, 2021, 10:48 a.m. by The FAIRsharing Team.

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EOSC-Life
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online documentation About
online documentation About Pfam
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Additional Information

Contact Robert D Finn

TeSS training resources 

Bioinformatics: Gene-protein-structure-function



Tools
HMMER3 http://hmmer.org v3.2.1

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Release

Download via FTP ftp://ftp.ebi.ac.uk/pub/databases/Pfam

Data Access

Browse http://pfam.xfam.org/browse
Search http://pfam.xfam.org/search

REST Web Services

REST web service http://pfam.xfam.org/help#tabview=tab11


Publications

The Pfam protein families database.

Finn RD., Mistry J., Tate J., Coggill P., Heger A., Pollington JE., Gavin OL., Gunasekaran P., Ceric G., Forslund K., Holm L., Sonnhammer EL., Eddy SR., Bateman A.,
Nucleic Acids Res. 2010

View Paper (PubMed) View Publication

The Pfam protein families database: towards a more sustainable future.

Finn RD,Coggill P,Eberhardt RY,Eddy SR,Mistry J,Mitchell AL,Potter SC,Punta M,Qureshi M,Sangrador-Vegas A,Salazar GA,Tate J,Bateman A
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

Pfam: the protein families database.

Finn RD,Bateman A,Clements J,Coggill P,Eberhardt RY,Eddy SR,Heger A,Hetherington K,Holm L,Mistry J,Sonnhammer EL,Tate J,Punta M
Nucleic Acids Res 2013

View Paper (PubMed) View Publication

The Pfam protein families database.

Punta M,Coggill PC,Eberhardt RY,Mistry J,Tate J,Boursnell C,Pang N,Forslund K,Ceric G,Clements J,Heger A,Holm L,Sonnhammer EL,Eddy SR,Bateman A,Finn RD
Nucleic Acids Res 2011

View Paper (PubMed) View Publication

The Pfam protein families database.

Finn RD,Tate J,Mistry J,Coggill PC,Sammut SJ,Hotz HR,Ceric G,Forslund K,Eddy SR,Sonnhammer EL,Bateman A
Nucleic Acids Res 2007

View Paper (PubMed) View Publication

Pfam: clans, web tools and services.

Finn RD,Mistry J,Schuster-Bockler B,Griffiths-Jones S,Hollich V,Lassmann T,Moxon S,Marshall M,Khanna A,Durbin R,Eddy SR,Sonnhammer EL,Bateman A
Nucleic Acids Res 2005

View Paper (PubMed) View Publication

Pfam: a comprehensive database of protein domain families based on seed alignments.

Sonnhammer EL,Eddy SR,Durbin R
Proteins 1997

View Paper (PubMed)

The Pfam protein families database in 2019.

El-Gebali S,Mistry J,Bateman A,Eddy SR,Luciani A,Potter SC,Qureshi M,Richardson LJ,Salazar GA,Smart A,Sonnhammer ELL,Hirsh L,Paladin L,Piovesan D,Tosatto SCE,Finn RD
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

Pfam: a comprehensive database of protein domain families based on seed alignments.

Sonnhammer EL,Eddy SR,Durbin R
Proteins 1997

View Paper (PubMed)

Pfam: The protein families database in 2021.

Mistry J,Chuguransky S,Williams L,Qureshi M,Salazar GA,Sonnhammer ELL,Tosatto SCE,Paladin L,Raj S,Richardson LJ,Finn RD,Bateman A
Nucleic Acids Res 2020

View Paper (PubMed) View Publication

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Credit

Record Maintainer

Funds

Maintains

Grant Number(s)

  • 108433/Z/15/Z (The Wellcome Trust, UK)

  • 654039 (EU Horizon 2020)

  • BB/L024136/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • BM1405 NGP-net (EuroKUP COST Action)

  • R01-HG009116 (National Human Genome Research Institute (NHGRI), Bethesda, MD, USA)

  • WT077044/Z/05/Z (The Wellcome Trust, UK)