The Pfam protein families database
База данных семейств белков Pfam
2009-11-17
SCID: 54.1/drvkeuu8
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HMMER3Pfam protein families databasePfam release 24.0profile hidden Markov modelsprotein domains
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Abstract (AI)
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/).
Key Findings
1
HMMER3 improves sensitivity through routine use of the forward algorithm, prompting substantial associated changes throughout Pfam.
2
Pfam is distributed through servers located in the UK, USA, and Sweden.
3
Pfam release 24.0 adopts HMMER3, enabling approximately 100-fold faster profile hidden Markov model searches than HMMER2.
4
Version 24.0 contains 11,912 protein families, with many families significantly updated over the preceding two years.
Research Object
The Pfam protein families and domains database (release 24.0)
Research Subject
Major database updates, including the use of HMMER3 and the resulting changes in family and domain annotation
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2009-11-17
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