Journal
NUCLEIC ACIDS RESEARCH
Volume 38, Issue -, Pages D211-D222Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkp985
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Funding
- Wellcome Trust [WT077044/Z/05/Z]
- Howard Hughes Medical Institute
- Stockholm University
- Royal Institute of Technology
- Swedish Natural Sciences Research Council
- Academy of Finland [114498]
- BBSRC [BB/F010435/1] Funding Source: UKRI
- MRC [MC_U137761446] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/F010435/1] Funding Source: researchfish
- Medical Research Council [MC_U137761446] Funding Source: researchfish
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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. This software is similar to 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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