The Pfam protein families database

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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. Thi...

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Autores principales: Finn, Robert D., Mistry, Jaina, Tate, John, Coggill, Penny, Heger, Andreas, Pollington, Joanne E., Gavin, O. Luke, Gunasekaran, Prasad, Ceric, Goran, Forslund, Kristoffer, Holm, Liisa, Sonnhammer, Erik L. L., Eddy, Sean R., Bateman, Alex
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Articles
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889/
https://www.ncbi.nlm.nih.gov/pubmed/19920124
http://dx.doi.org/10.1093/nar/gkp985
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author Finn, Robert D.
Mistry, Jaina
Tate, John
Coggill, Penny
Heger, Andreas
Pollington, Joanne E.
Gavin, O. Luke
Gunasekaran, Prasad
Ceric, Goran
Forslund, Kristoffer
Holm, Liisa
Sonnhammer, Erik L. L.
Eddy, Sean R.
Bateman, Alex
author_facet Finn, Robert D.
Mistry, Jaina
Tate, John
Coggill, Penny
Heger, Andreas
Pollington, Joanne E.
Gavin, O. Luke
Gunasekaran, Prasad
Ceric, Goran
Forslund, Kristoffer
Holm, Liisa
Sonnhammer, Erik L. L.
Eddy, Sean R.
Bateman, Alex
author_sort Finn, Robert D.
collection PubMed
description 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 ∼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/).
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spelling pubmed-28088892010-01-20 The Pfam protein families database Finn, Robert D. Mistry, Jaina Tate, John Coggill, Penny Heger, Andreas Pollington, Joanne E. Gavin, O. Luke Gunasekaran, Prasad Ceric, Goran Forslund, Kristoffer Holm, Liisa Sonnhammer, Erik L. L. Eddy, Sean R. Bateman, Alex Nucleic Acids Res Articles 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 ∼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/). Oxford University Press 2010-01 2009-11-17 /pmc/articles/PMC2808889/ /pubmed/19920124 http://dx.doi.org/10.1093/nar/gkp985 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Finn, Robert D.
Mistry, Jaina
Tate, John
Coggill, Penny
Heger, Andreas
Pollington, Joanne E.
Gavin, O. Luke
Gunasekaran, Prasad
Ceric, Goran
Forslund, Kristoffer
Holm, Liisa
Sonnhammer, Erik L. L.
Eddy, Sean R.
Bateman, Alex
The Pfam protein families database
title The Pfam protein families database
title_full The Pfam protein families database
title_fullStr The Pfam protein families database
title_full_unstemmed The Pfam protein families database
title_short The Pfam protein families database
title_sort pfam protein families database
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889/
https://www.ncbi.nlm.nih.gov/pubmed/19920124
http://dx.doi.org/10.1093/nar/gkp985
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