2010, Vol. 38, Database issue | 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, Sean R. Eddy, Alex Bateman
Pfam is a widely used database of protein families and domains. This article describes major updates in the latest release (version 24.0), including the adoption of HMMER3, a faster and more sensitive profile hidden Markov model package. Pfam release 24.0 contains 11,912 families, with significant updates to many families over the past two years. The move to HMMER3 has necessitated numerous changes to Pfam, including improvements in sequence and residue coverage, increased sensitivity, and streamlined database and web services. Pfam is available via servers in the UK, USA, and Sweden. The article also discusses the improvements in the Pfam pipeline, such as the use of FastTree for neighbor-joining trees, the addition of interactive sequence searches, and the integration of TreeFam links. Additionally, the article highlights the improvements in scientific annotations, DAS ontology compliance, and the local Pfam search tool, pfam_scan. The Xfam blog is used to communicate changes and progress to the Pfam community. Despite some incompatibility issues with older versions of HMMER, the authors believe that the benefits of HMMER3 outweigh the drawbacks.Pfam is a widely used database of protein families and domains. This article describes major updates in the latest release (version 24.0), including the adoption of HMMER3, a faster and more sensitive profile hidden Markov model package. Pfam release 24.0 contains 11,912 families, with significant updates to many families over the past two years. The move to HMMER3 has necessitated numerous changes to Pfam, including improvements in sequence and residue coverage, increased sensitivity, and streamlined database and web services. Pfam is available via servers in the UK, USA, and Sweden. The article also discusses the improvements in the Pfam pipeline, such as the use of FastTree for neighbor-joining trees, the addition of interactive sequence searches, and the integration of TreeFam links. Additionally, the article highlights the improvements in scientific annotations, DAS ontology compliance, and the local Pfam search tool, pfam_scan. The Xfam blog is used to communicate changes and progress to the Pfam community. Despite some incompatibility issues with older versions of HMMER, the authors believe that the benefits of HMMER3 outweigh the drawbacks.