The Pfam protein families database.

Nucleic Acids Research
Robert D FinnAlex Bateman

Abstract

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 11, 1999·Nucleic Acids Research·A BatemanE L Sonnhammer
Apr 5, 2002·Genome Research·W James Kent
Nov 9, 2002·Bioinformatics·Kevin HoweRichard Durbin
Jan 23, 2004·BMC Bioinformatics·Benjamin Schuster-BöcklerSven Rahmann
Nov 9, 2004·Bioinformatics·Johannes Söding
Dec 21, 2004·Nucleic Acids Research·Andreas HegerLiisa Holm
Dec 31, 2005·Nucleic Acids Research·Cathy H WuBaris Suzek
Dec 31, 2005·Nucleic Acids Research·Robert D FinnAlex Bateman
Feb 6, 2007·Bioinformatics·Alex Bateman, Robert D Finn
Aug 11, 2007·BMC Bioinformatics·Jaina MistryRobert D Finn
Nov 8, 2007·Nucleic Acids Research·Andreas HegerLiisa Holm
Nov 15, 2007·Nucleic Acids Research·Antonina AndreevaAlexey G Murzin
Nov 21, 2007·Methods in Molecular Biology·Jaina Mistry, Robert Finn
Dec 7, 2007·Nucleic Acids Research·Jue RuanRichard Durbin
Dec 13, 2007·Nucleic Acids Research·Kim HenrickHelen M Berman
Jun 3, 2008·Nucleic Acids Research·J Lynn FinkPhilip E Bourne
Oct 22, 2008·Bioinformatics·Gabrielle A ReevesJanet M Thornton
Oct 23, 2008·Nucleic Acids Research·Sarah HunterCorin Yeats
Oct 28, 2008·Nucleic Acids Research·Paul P GardnerAlex Bateman
Apr 21, 2009·Molecular Biology and Evolution·Morgan N PriceAdam P Arkin

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Citations

May 30, 2013·Archives of Microbiology·Adolfo López-EsparzaArturo Flores-Carreón
Mar 26, 2011·Journal of Molecular Evolution·Varinia López-RamírezGabriela Olmedo-Álvarez
Nov 19, 2010·Applied Microbiology and Biotechnology·Jonathan E SchmitzVincent A Fischetti
Jul 20, 2010·Biotechnology Letters·Katty Goossens, Ronnie Willaert
Mar 30, 2011·Journal of Structural and Functional Genomics·Elchin S JulfayevWilliam A McLaughlin
Apr 8, 2011·Journal of Structural and Functional Genomics·Margaret J GabanyiHelen M Berman
Jul 26, 2011·Journal of Structural and Functional Genomics·Alexander EletskyThomas Szyperski
Jan 25, 2012·Journal of Structural and Functional Genomics·Elchin S JulfayevWilliam A McLaughlin
Jan 25, 2012·Journal of Structural and Functional Genomics·Lee SaelDaisuke Kihara
May 18, 2012·Journal of Structural and Functional Genomics·James M AraminiGaetano T Montelione
Aug 27, 2013·Photosynthesis Research·S KrishnakumarGanesh A Viswanathan
Apr 10, 2013·Progress in Biophysics and Molecular Biology·Liane GaboraStuart Kauffman
Nov 2, 2011·Accounts of Chemical Research·David E Cane, Haruo Ikeda
Aug 3, 2010·Biochemistry·Matthew E TraversoAmy C Rosenzweig
May 16, 2012·Biochemistry·Angela S FleischhackerPatricia J Kiley
Aug 30, 2012·Journal of the American Chemical Society·David W RooklinYingkai Zhang
Dec 29, 2012·Journal of the American Chemical Society·Avena C RossBradley S Moore
Jul 9, 2010·The ISME Journal·Melissa Beth DuhaimeFrank Oliver Glöckner
Dec 16, 2011·The ISME Journal·Chris L DupontJ Craig Venter
Feb 3, 2012·The ISME Journal·Michael LiuTorsten Thomas
Jul 22, 2011·Nature·Alistair B RussellJoseph D Mougous
Jul 6, 2012·Nature·Patrick R H SteinmetzUlrich Technau
Aug 9, 2013·Nature·Mikhail M ShneiderPetr G Leiman

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Software Mentioned

BLAST
PRC
javascript
PRODOM
HMMER
Open Protein Structure Annotation Network ( TOPSAN )
VMX
GenPept
HHsearch
TOPSAN

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