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Significant expansion of exon-bordering protein domains during animal proteome evolution

Oxford University Press
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gkj149 247..251 Pfam: clans, web tools and services Robert D. Finn*, Jaina Mistry, Benjamin Schuster-Bo¨ckler, Sam Griffiths-Jones, Volker Hollich1, Timo Lassmann1, Simon Moxon, Mhairi Marshall, Ajay Khanna2, Richard Durbin, Sean R. Eddy2, Erik L. L. Sonnhammer1 and Alex Bateman Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK, 1Center for Genomics and Bioinformatics, Karolinska Institutet, S-171 77 Stockholm, Sweden and 2Department of Genetics, Howard Hughes Medical Institute, Washington University School of Medicine, St Louis, MO 63110, USA Received September 15, 2005; Revised October 19, 2005; Accepted October 28, 2005 ABSTRACT Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent devel- opment in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow program- matic access to the database andassociated tools are also presented. Pfam is available on theweb in theUK (, the USA (, France (http://pfam.jouy. and Sweden ( INTRODUCTION Pfam is a comprehensive database of protein families, con- taining 7973 families in the current release (18.0). Each family is manually curated and is represented by two multiple sequence alignments, two profile-Hidden Markov Models (profile-HMMs) and an annotation file. All data are available for download in flatfile format from the FTP sites linked from each Pfam website and also as a set of MySQL relational database files. Pfam families are periodically updated with each family having on average been modified four times since its creation. The data and additional features are access- ible via the four websites ( Pfam/,, http://pfa

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