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Pfam

Recommended

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:

Sanger Pfam Mirror

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

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

Evolutionary relationship between proteins via sequence similarity

In the following recommendations:

How to cite this record FAIRsharing.org: Pfam; Pfam; DOI: https://doi.org/10.25504/FAIRsharing.y3scf6; Last edited: Feb. 12, 2020, 7:24 p.m.; Last accessed: Apr 07 2020 8:28 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. 12, 2020, 7:24 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.y3scf6' by 'The FAIRsharing Team' at 19:24, 12 Feb 2020 (approved):

	'organizations' has been modified:
		Before:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			EU Horizon 2020|https://ec.europa.eu/programmes/horizon2020/|Funds
			EuroKUP COST Action|http://www.eurokup.org|Funds
			National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds
			Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK|http://www.sanger.ac.uk|Maintains
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA|https://www.mcb.harvard.edu|Maintains
			Stockholm University, Sweden|https://www.sbc.su.se|Maintains
		After:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			EU Horizon 2020|https://ec.europa.eu/programmes/horizon2020/|Funds
			EuroKUP COST Action|http://www.eurokup.org|Funds
			National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds
			Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK|http://www.sanger.ac.uk|Maintains
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA|https://www.mcb.harvard.edu|Maintains
			Stockholm University, Sweden|https://www.sbc.su.se|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:

	'supportLinks' has been modified:
		Before:
			FAQ|http://pfam.xfam.org/help#helpFAQBlock
			blog|https://xfam.wordpress.com/
			email|pfam-help@ebi.ac.uk
			help|http://pfam.xfam.org/help
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			mailing list|pfamlist-subscribe@ebi.ac.uk
			online documentation|http://pfam.xfam.org/about
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		After:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			blog|http://xfam.wordpress.com/tag/pfam/
			email|pfam-help@ebi.ac.uk
			help|http://pfam.xfam.org/help
			mailing list|pfamlist-subscribe@ebi.ac.uk
			online documentation|http://pfam.xfam.org/about
			online documentation|http://pfam.xfam.org/about
			rss|http://xfam.wordpress.com/tag/pfam/feed/
			tess training|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			training|http://pfam.xfam.org/help#tabview=tab3
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		Added:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			blog|http://xfam.wordpress.com/tag/pfam/
			rss|http://xfam.wordpress.com/tag/pfam/feed/
			tess training|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			training|http://pfam.xfam.org/help#tabview=tab3
		Removed:
			FAQ|http://pfam.xfam.org/help#helpFAQBlock
			blog|https://xfam.wordpress.com/
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/

	'countries' has been modified:
		Before:
			United Kingdom
		After:
			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
		Added:
			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 States
		Removed:

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Biology
		Added:
			Biology
		Removed:
			Life Science

	'dataProcesses' has been modified:
		Before:
			file download(txt)
			SQL database dump
			DAS server
			FTP download
			browse
			Search
		After:
			Download via FTP
			Browse
			Search
		Added:
			Download via FTP
			Browse
		Removed:
			file download(txt)
			SQL database dump
			DAS server
			FTP download
			browse

	'accessPoints' has been modified:
		Before:
			REST|http://pfam.xfam.org/help#helpRestBlock|REST web service
		After:
			REST|http://pfam.xfam.org/help#tabview=tab11|REST web service
		Added:
			REST|http://pfam.xfam.org/help#tabview=tab11|REST web service
		Removed:
			REST|http://pfam.xfam.org/help#helpRestBlock|REST web service

	'tools' has been modified:
		Before:
			HUMMER|v3.2.1|http://hmmer.org
		After:
			HMMER3|v3.2.1|http://hmmer.org
		Added:
			HMMER3|v3.2.1|http://hmmer.org
		Removed:
			HUMMER|v3.2.1|http://hmmer.org

Edits to 'https://fairsharing.org/FAIRsharing.y3scf6' by 'The FAIRsharing Team' at 20:20, 14 Mar 2019 (approved):

	'contactEmail' has been modified:
		Before: pfam-help@ebi.ac.uk
		After: rdf@ebi.ac.uk

	'contact' has been modified:
		Before: General contact
		After: Robert D Finn

	'supportLinks' has been modified:
		Before:
			FAQ|http://pfam.xfam.org/help#helpFAQBlock
			blog|https://xfam.wordpress.com/
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			help|http://pfam.xfam.org/help
			mailing list|pfamlist-subscribe@ebi.ac.uk
			online documentation|http://pfam.xfam.org/about
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		After:
			FAQ|http://pfam.xfam.org/help#helpFAQBlock
			blog|https://xfam.wordpress.com/
			email|pfam-help@ebi.ac.uk
			help|http://pfam.xfam.org/help
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			mailing list|pfamlist-subscribe@ebi.ac.uk
			online documentation|http://pfam.xfam.org/about
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		Added:
			email|pfam-help@ebi.ac.uk
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.y3scf6' by 'The FAIRsharing Team' at 20:16, 14 Mar 2019 (approved):

	'organizations' has been modified:
		Before:
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK|http://www.sanger.ac.uk|Maintains
			Howard Hughes Medical Institute|https://www.hhmi.org/|Undefined
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA|https://www.mcb.harvard.edu|Undefined
			Stockholm University, Sweden|https://www.sbc.su.se|Undefined
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		After:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			European Molecular Biology Laboratory (EMBL), Heidelberg, Germany|http://www.embl.org|Funds
			Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK|http://www.sanger.ac.uk|Maintains
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA|https://www.mcb.harvard.edu|Maintains
			Stockholm University, Sweden|https://www.sbc.su.se|Maintains
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			EU Horizon 2020|https://ec.europa.eu/programmes/horizon2020/|Funds
			EuroKUP COST Action|http://www.eurokup.org|Funds
			National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds
		Added:
			Howard Hughes Medical Institute|https://www.hhmi.org/|Maintains
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA|https://www.mcb.harvard.edu|Maintains
			Stockholm University, Sweden|https://www.sbc.su.se|Maintains
			EU Horizon 2020|https://ec.europa.eu/programmes/horizon2020/|Funds
			EuroKUP COST Action|http://www.eurokup.org|Funds
			National Human Genome Research Institute (NHGRI), Bethesda, MD, USA|http://www.genome.gov/|Funds
		Removed:
			Howard Hughes Medical Institute|https://www.hhmi.org/|Undefined
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA|https://www.mcb.harvard.edu|Undefined
			Stockholm University, Sweden|https://www.sbc.su.se|Undefined
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds

	'supportLinks' has been modified:
		Before:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			blog|https://xfam.wordpress.com/
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			help|http://pfam.xfam.org/help
			help|http://pfam.xfam.org/help#tabview=tab3
			mailing list|pfamlist-subscribe@ebi.ac.uk
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		After:
			FAQ|http://pfam.xfam.org/help#helpFAQBlock
			blog|https://xfam.wordpress.com/
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			help|http://pfam.xfam.org/help
			mailing list|pfamlist-subscribe@ebi.ac.uk
			online documentation|http://pfam.xfam.org/about
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		Added:
			FAQ|http://pfam.xfam.org/help#helpFAQBlock
			online documentation|http://pfam.xfam.org/about
		Removed:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			help|http://pfam.xfam.org/help#tabview=tab3

	'onto_domains' has been modified:
		Before:
			Biological Evolution
			Function analysis
			Prediction and recognition
			Protein domain
			Protein sequence
			Sequence similarity
			protein
		After:
			Biocuration
			Biological Evolution
			Function analysis
			Hidden Markov model
			Multiple sequence alignment
			Prediction and recognition
			Protein Binding Domain
			Protein domain
			Protein sequence
			Sequence alignment
			Sequence motif
			Sequence similarity
			functional domain
			protein
			proteome
		Added:
			Biocuration
			Hidden Markov model
			Multiple sequence alignment
			Protein Binding Domain
			Sequence alignment
			Sequence motif
			functional domain
			proteome
		Removed:

	'grants' has been modified:
		Before:
			108433/Z/15/Z
			BB/L024136/1
			WT077044/Z/05/Z
		After:
			108433/Z/15/Z
			654039
			BB/L024136/1
			BM1405 NGP-net
			R01-HG009116
			WT077044/Z/05/Z
		Added:
			654039
			BM1405 NGP-net
			R01-HG009116
		Removed:

	'publications' has been modified:
		Before:
			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
			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
			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
			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
			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
			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
			Pfam: a comprehensive database of protein domain families based on seed alignments.|Sonnhammer EL,Eddy SR,Durbin R|Proteins|1997
		After:
			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
			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
			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
			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
			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
			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
			Pfam: a comprehensive database of protein domain families based on seed alignments.|Sonnhammer EL,Eddy SR,Durbin R|Proteins|1997
			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
			Pfam: a comprehensive database of protein domain families based on seed alignments.|Sonnhammer EL,Eddy SR,Durbin R|Proteins|1997
		Added:
			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
		Removed:

	'accessPoints' has been modified:
		Before:
			REST|http://pfam.xfam.org/help#tabview=tab10|REST web service
		After:
			REST|http://pfam.xfam.org/help#helpRestBlock|REST web service
		Added:
			REST|http://pfam.xfam.org/help#helpRestBlock|REST web service
		Removed:
			REST|http://pfam.xfam.org/help#tabview=tab10|REST web service

	'tools' has been modified:
		Before:
			HUMMER||http://hmmer.org
		After:
			HUMMER|v3.2.1|http://hmmer.org
		Added:
			HUMMER|v3.2.1|http://hmmer.org
		Removed:
			HUMMER||http://hmmer.org

Edits to 'https://fairsharing.org/FAIRsharing.y3scf6' by 'The FAIRsharing Team' at 11:02, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Amino acid sequence
			Biological evolution
			Evolutionary relationship between proteins via sequence similarity
			Function analysis
			Life Science
			Prediction and recognition
			Protein
			Protein domain
			Sequence similarity
		After:
			Amino acid sequence
			Biological evolution
			Computational predictions
			Evolutionary relationship between proteins via sequence similarity
			Function analysis
			Life Science
			Protein
			Protein domain
			Sequence similarity
		Added:
			Computational predictions
		Removed:
			Prediction and recognition

Edits to 'https://fairsharing.org/FAIRsharing.y3scf6' by 'The FAIRsharing Team' at 09:53, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Biological evolution
			Evolutionary relationship between proteins via sequence similarity
			Function analysis
			Life Science
			Prediction and recognition
			Protein
			Protein domain
			Sequence similarity
		After:
			Amino acid sequence
			Biological evolution
			Evolutionary relationship between proteins via sequence similarity
			Function analysis
			Life Science
			Prediction and recognition
			Protein
			Protein domain
			Sequence similarity
		Added:
			Amino acid sequence
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.y3scf6' by 'The FAIRsharing Team' at 10:22, 13 Aug 2018 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			blog|https://xfam.wordpress.com/
			help|http://pfam.xfam.org/help
			help|http://pfam.xfam.org/help#tabview=tab3
			mailing list|pfamlist-subscribe@ebi.ac.uk
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			tess training|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		After:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			blog|https://xfam.wordpress.com/
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			help|http://pfam.xfam.org/help
			help|http://pfam.xfam.org/help#tabview=tab3
			mailing list|pfamlist-subscribe@ebi.ac.uk
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		Added:
			help|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
		Removed:
			tess training|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function

Edits to 'https://fairsharing.org/FAIRsharing.y3scf6' by 'The FAIRsharing Team' at 20:05, 04 Aug 2018 (approved):

	'organizations' has been modified:
		Before:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK|http://www.sanger.ac.uk|Maintains
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
		After:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
			Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK|http://www.sanger.ac.uk|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom|https://www.ebi.ac.uk/|Funds
			Howard Hughes Medical Institute|https://www.hhmi.org/|Undefined
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA |https://www.mcb.harvard.edu|Undefined
			Stockholm University|https://www.sbc.su.se|Undefined
			The Wellcome Trust|https://wellcome.ac.uk/|Funds
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom|https://www.ebi.ac.uk/|Funds
			Howard Hughes Medical Institute|https://www.hhmi.org/|Undefined
			Department of Molecular and Cell Biology, Harvard University, Cambridge, USA |https://www.mcb.harvard.edu|Undefined
			Stockholm University|https://www.sbc.su.se|Undefined
			The Wellcome Trust|https://wellcome.ac.uk/|Funds
		Removed:

	'supportLinks' has been modified:
		Before:
			blog|https://xfam.wordpress.com/
			help|http://pfam.xfam.org/help#tabview=tab3
			help|http://pfam.xfam.org/help
			mailing list|pfamlist-subscribe@ebi.ac.uk
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		After:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			blog|https://xfam.wordpress.com/
			help|http://pfam.xfam.org/help
			help|http://pfam.xfam.org/help#tabview=tab3
			mailing list|pfamlist-subscribe@ebi.ac.uk
			rss|https://xfam.wordpress.com/tag/pfam/feed/
			tess training|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
			twitter|@Xfam_EBI
			wikipedia|https://en.wikipedia.org/wiki/Pfam
		Added:
			FAQ|http://pfam.xfam.org/help#tabview=tab4
			tess training|https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function
			training|https://xfam.wordpress.com/2016/12/08/pfam-train-online/
		Removed:

	'name' has been modified:
		Before: Pfam Protein Families
		After: Pfam

	'licences' has been modified:
		Before:
			Creative Commons Attribution 3.0 Unported (CC BY 3.0)|https://creativecommons.org/licenses/by/3.0/|Data
		After:
			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data
		Added:
			Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication|https://creativecommons.org/publicdomain/zero/1.0/|Data
		Removed:
			Creative Commons Attribution 3.0 Unported (CC BY 3.0)|https://creativecommons.org/licenses/by/3.0/|Data

	'dataProcesses' has been modified:
		Before:
			browse
			search
			file download(txt)
			SQL database dump
			DAS server
			FTP download
		After:
			browse
			file download(txt)
			SQL database dump
			DAS server
			FTP download
			Search
		Added:
			Search
		Removed:
			search

	'contact' has been modified:
		Before: 
		After: General contact

	'publications' has been modified:
		Before:
			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
			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
		After:
			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
			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
			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
			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
			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
			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
			Pfam: a comprehensive database of protein domain families based on seed alignments.|Sonnhammer EL,Eddy SR,Durbin R|Proteins|1997
		Added:
			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
			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
			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
			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
			Pfam: a comprehensive database of protein domain families based on seed alignments.|Sonnhammer EL,Eddy SR,Durbin R|Proteins|1997
		Removed:

	'tools' has been modified:
		Before:
			Search||http://pfam.xfam.org/search
		After:
			HUMMER||http://hmmer.org
		Added:
			HUMMER||http://hmmer.org
		Removed:
			Search||http://pfam.xfam.org/search

	'description' has been modified:
		Before: The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function.

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.
		After: 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.

Support

General

FAQ	FAQ
blog	Pfam Blog
support email	HelpDesk
help	Help Pages
Mailing List	None
online documentation	About Pfam
online documentation	About
rss	RSS Feed
training	Online Training
twitter	@Xfam_EBI
wikipedia	Wikipedia Entry

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

Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

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