title: The Pfam protein families database.
abstract: Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the 'sunburst' representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.
authors: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. mp13@sanger.ac.uk
authors: Marco
authors: M
authors: Punta
authors: Penny C
authors: PC
authors: Coggill
authors: Ruth Y
authors: RY
authors: Eberhardt
authors: Jaina
authors: J
authors: Mistry
authors: John
authors: J
authors: Tate
authors: Chris
authors: C
authors: Boursnell
authors: Ningze
authors: N
authors: Pang
authors: Kristoffer
authors: K
authors: Forslund
authors: Goran
authors: G
authors: Ceric
authors: Jody
authors: J
authors: Clements
authors: Andreas
authors: A
authors: Heger
authors: Liisa
authors: L
authors: Holm
authors: Erik L L
authors: EL
authors: Sonnhammer
authors: Sean R
authors: SR
authors: Eddy
authors: Alex
authors: A
authors: Bateman
authors: Robert D
authors: RD
authors: Finn
mesh_terms: D030562:Databases, Protein; D004690:Encyclopedias as Topic; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000145:classification*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins