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The Pfam protein families database

Robert D. Finn, Jaina Mistry, John Tate, Penny Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer (+2 others)
2009 Nucleic Acids Research  
The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14.  ...  Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models.  ...  ACKNOWLEDGEMENTS We are grateful to the many people who have submitted data to Pfam. In particular, William Mifsud, Matthew Bashton and Nina Mian have added many of the new families in Pfam.  ... 
doi:10.1093/nar/gkp985 pmid:19920124 pmcid:PMC2808889 fatcat:kq2gbc364zfevfvpnw4fk3i5w4

Pfam: the protein families database [chapter]

Robert D. Finn
2005 Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics  
Pfam, available via servers in the UK (http://pfam. sanger.ac.uk/) and the USA (http://pfam.janelia. org/), is a widely used database of protein families, containing 14 831 manually curated entries in  ...  of the underlying sequence database.  ...  One of the distinguishing features of Pfam compared with most other protein family databases is our provision of full alignments.  ... 
doi:10.1002/047001153x.g306303 fatcat:3hajpm6bwjfblifyjxiroehrui

The Pfam protein families database

A. Bateman
2004 Nucleic Acids Research  
(D) DUF families and protein structure.  ...  ACKNOWLEDGEMENTS We are grateful for the infrastructure support provided by the Systems, Web and Database administration teams at (C) Co-occurrence between DUFs and other families.  ...  CONCLUDING REMARKS Pfam is a database of protein sequence families.  ... 
doi:10.1093/nar/gkh121 pmid:14681378 pmcid:PMC308855 fatcat:cnj7bwfs25huji2jaihj2x7fsi

The Pfam protein families database

M. Punta, P. C. Coggill, R. Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, J. Clements, A. Heger, L. Holm (+4 others)
2011 Nucleic Acids Research  
Pfam, available via servers in the UK (http://pfam. sanger.ac.uk/) and the USA (http://pfam.janelia. org/), is a widely used database of protein families, containing 14 831 manually curated entries in  ...  of the underlying sequence database.  ...  One of the distinguishing features of Pfam compared with most other protein family databases is our provision of full alignments.  ... 
doi:10.1093/nar/gkr1065 pmid:22127870 pmcid:PMC3245129 fatcat:rtmlicy2zzeqvjylnnhtrmnzki

Pfam: the protein families database

Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John Tate (+1 others)
2013 Nucleic Acids Research  
Pfam, available via servers in the UK (http://pfam. sanger.ac.uk/) and the USA (http://pfam.janelia. org/), is a widely used database of protein families, containing 14 831 manually curated entries in  ...  of the underlying sequence database.  ...  One of the distinguishing features of Pfam compared with most other protein family databases is our provision of full alignments.  ... 
doi:10.1093/nar/gkt1223 pmid:24288371 pmcid:PMC3965110 fatcat:bpi3hvlmdzh4ha52uaz2xpwdru

The Pfam Protein Families Database

A. Bateman
2002 Nucleic Acids Research  
The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14.  ...  Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models.  ...  ACKNOWLEDGEMENTS We are grateful to the many people who have submitted data to Pfam. In particular, William Mifsud, Matthew Bashton and Nina Mian have added many of the new families in Pfam.  ... 
doi:10.1093/nar/30.1.276 pmid:11752314 pmcid:PMC99071 fatcat:mrvo43wg75bodhl25x6z373kiy

The Pfam Protein Families Database

A. Bateman
2000 Nucleic Acids Research  
The latest version (4.3) of Pfam contains 1815 families. These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9.  ...  For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package.  ...  In particular we thank Matthew Bashton who added many of the new families in Pfam, Christian Storm for writing NIFAS, and Michael Åsman and Mats Jonsson for adding new features to the websites.  ... 
doi:10.1093/nar/28.1.263 pmid:10592242 pmcid:PMC102420 fatcat:qf5w6rqz3jh2tparq7622etwpm

The Pfam protein families database

R. D. Finn, J. Tate, J. Mistry, P. C. Coggill, S. J. Sammut, H.-R. Hotz, G. Ceric, K. Forslund, S. R. Eddy, E. L. L. Sonnhammer, A. Bateman
2007 Nucleic Acids Research  
(D) DUF families and protein structure.  ...  ACKNOWLEDGEMENTS We are grateful for the infrastructure support provided by the Systems, Web and Database administration teams at (C) Co-occurrence between DUFs and other families.  ...  CONCLUDING REMARKS Pfam is a database of protein sequence families.  ... 
doi:10.1093/nar/gkm960 pmid:18039703 pmcid:PMC2238907 fatcat:62zovw7qerfv7od2ctaan5efty

Pfam: The protein families database in 2021

Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A Salazar, Erik L L Sonnhammer, Silvio C E Tosatto, Lisanna Paladin, Shriya Raj, Lorna J Richardson, Robert D Finn, Alex Bateman
2020 Nucleic Acids Research  
The Pfam database is a widely used resource for classifying protein sequences into families and domains.  ...  We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families.  ...  We are grateful to Layla Hirsh Martinez and Aleix Lafita for adding families to Pfam and to the numerous scientists who contributed suggestions and families via our helpdesk. FUNDING  ... 
doi:10.1093/nar/gkaa913 pmid:33125078 pmcid:PMC7779014 fatcat:qhulduagfrg2jj7n25n5sppaue

The Pfam protein families database in 2019

Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart, Erik L L Sonnhammer, Layla Hirsh (+4 others)
2018 Nucleic Acids Research  
We carried out a significant comparison to the structural classification database, namely the Evolutionary Classification of Protein Domains (ECOD) that led to the creation of 825 new families based on  ...  We recently began to collaborate with the RepeatsDB resource to improve the definition of tandem repeat families within Pfam.  ...  ACKNOWLEDGEMENTS We would like to thank the various members of the EMBL-European Bioinformatics Institute training team for their assistance in developing the online training materials.  ... 
doi:10.1093/nar/gky995 pmid:30357350 pmcid:PMC6324024 fatcat:q5wtvxfqzzhobpis5p4d2g6wue

The Pfam protein families database: towards a more sustainable future

Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John Tate (+1 others)
2015 Nucleic Acids Research  
In the last two years the Pfam database (http://pfam. xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases.  ...  Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved.  ...  INTRODUCTION While sequence databases are growing at exponential rates, protein family databases such as Pfam are growing at a roughly linear rate (1) .  ... 
doi:10.1093/nar/gkv1344 pmid:26673716 pmcid:PMC4702930 fatcat:o7rimhdmlrawdjm6ahqj3yfyhe

The TIGRFAMs database of protein families

D. H. Haft
2003 Nucleic Acids Research  
The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs.  ...  and pointers to related TIGRFAMs, Pfam and InterPro models.  ...  INTRODUCTION TIGRFAMs is a manually curated database of protein families described by hidden Markov models (HMMs) and attached information. It is available by FTP and through the World Wide Web.  ... 
doi:10.1093/nar/gkg128 pmid:12520025 pmcid:PMC165575 fatcat:ljk4hkntfff7tnufkmyp7erd5q

The SYSTERS Protein Family Database in 2005

T. Meinel
2004 Nucleic Acids Research  
To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server.  ...  The SYSTERS web server (http://systers.molgen. mpg.de) provides access to 158 153 SYSTERS protein families.  ...  ACKNOWLEDGEMENTS We acknowledge funding from Bundesministerium f€ u ur Bildung und Forschung (BMBF) through the Helmholtz Network for Bioinformatics (HNB).  ... 
doi:10.1093/nar/gki030 pmid:15608183 pmcid:PMC539984 fatcat:umlfcktubncynjllv2xlmesvzu

The Protein Family Classification in Protein Databases via Entropy Measures [article]

R.P. Mondaini, S.C. de Albuquerque Neto
2018 arXiv   pre-print
An intensive study of the Pfam databases is presented with restrictions to families which could be represented by rectangular arrays of amino acids with m rows (protein domains) and n columns (amino acids  ...  In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases.  ...  We then give below the results of checking the inequalities (50) for some families of the Pfam database.  ... 
arXiv:1806.05172v1 fatcat:zuuykcfekzbx5ljha4urnpy35q

The InterPro protein families and domains database: 20 years on

Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar (+21 others)
2020 Nucleic Acids Research  
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites.  ...  Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases.  ...  ACKNOWLEDGEMENTS The authors would like to thank former members of the InterPro team: Sara El-Gebali, Matthew Fraser, Aurélien Luciani, Sebastien Pesseat, Simon Potter, Neil Rawlings, Amaia Sangrador-Vegas  ... 
doi:10.1093/nar/gkaa977 pmid:33156333 pmcid:PMC7778928 fatcat:vfs7k3dxr5bcpbpvxbptj6r46m
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