title: Pfam: the protein families database.
abstract: Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures.
authors.affiliation: HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 (Viikinkaari 5), 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Finn
authors.forename: Alex
authors.initials: A
authors.lastname: Bateman
authors.forename: Jody
authors.initials: J
authors.lastname: Clements
authors.forename: Penelope
authors.initials: P
authors.lastname: Coggill
authors.forename: Ruth Y
authors.initials: RY
authors.lastname: Eberhardt
authors.forename: Sean R
authors.initials: SR
authors.lastname: Eddy
authors.forename: Andreas
authors.initials: A
authors.lastname: Heger
authors.forename: Kirstie
authors.initials: K
authors.lastname: Hetherington
authors.forename: Liisa
authors.initials: L
authors.lastname: Holm
authors.forename: Jaina
authors.initials: J
authors.lastname: Mistry
authors.forename: Erik L L
authors.initials: EL
authors.lastname: Sonnhammer
authors.forename: John
authors.initials: J
authors.lastname: Tate
authors.forename: Marco
authors.initials: M
authors.lastname: Punta
mesh_terms: D030562:Databases, Protein; D020407:Internet; D064267:Intrinsically Disordered Proteins / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D020543:Proteome / Q000737:chemistry; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
chemical_list: D064267:Intrinsically Disordered Proteins; D011506:Proteins; D020543:Proteome