Media type: E-Article Title: Identifying Protein Domains with the Pfam Database Contributor: Coggill, Penny; Finn, Robert D.; Bateman, Alex imprint: Wiley, 2008 Published in: Current Protocols in Bioinformatics Language: English DOI: 10.1002/0471250953.bi0205s23 ISSN: 1934-3396; 1934-340X Keywords: Biochemistry ; Structural Biology Origination: Footnote: Description: <jats:title>Abstract</jats:title><jats:p>Pfam is a database of protein domain families, with each family represented by multiple sequence alignments and profile hidden Markov models (HMMs). In addition, each family has associated annotation, literature references, and links to other databases. The entries in Pfam are available via the World Wide Web and in flatfile format. This unit contains detailed information on how to access and utilize the information present in the Pfam database, namely the families, multiple alignments, and annotation. Details on running Pfam, both remotely and locally are presented. <jats:italic>Curr. Protoc. Bioinform</jats:italic>. 23:2.5.1‐2.5.17. © 2008 by John Wiley & Sons, Inc.</jats:p>