title: Identifying protein domains with the Pfam database.
abstract: 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.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Penny
authors.initials: P
authors.lastname: Coggill
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Finn
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Alex
authors.initials: A
authors.lastname: Bateman
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020407:Internet; D008390:Markov Chains; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D011506:Proteins