@article {6886,
	title = {Pfam: the protein families database.},
	journal = {Nucleic acids research},
	volume = {42},
	year = {2014},
	month = {2014 Jan},
	pages = {D222-30},
	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.},
	keywords = {Databases, DNA, Internet, Intrinsically Disordered Proteins, Protein, Protein Conformation, Proteins, Proteome, Sequence Alignment, Sequence Analysis},
	issn = {1362-4962},
	doi = {10.1093/nar/gkt1223},
	author = {Finn, Robert D and Bateman, Alex and Clements, Jody and Coggill, Penelope and Eberhardt, Ruth Y and Sean R. Eddy and Heger, Andreas and Hetherington, Kirstie and Holm, Liisa and Mistry, Jaina and Sonnhammer, Erik L L and Tate, John and Punta, Marco}
}
@article {6272,
	title = {Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.},
	journal = {Nucleic Acids Research},
	volume = {41},
	year = {2013},
	month = {2013 Jul},
	pages = {e121},
	abstract = {<p>Detection of protein homology via sequence similarity has important applications in biology, from protein structure and function prediction to reconstruction of phylogenies. Although current methods for aligning protein sequences are powerful, challenges remain, including problems with homologous overextension of alignments and with regions under convergent evolution. Here, we test the ability of the profile hidden Markov model method HMMER3 to correctly assign homologous sequences to \&gt;13,000 manually curated families from the Pfam database. We identify problem families using protein regions that match two or more Pfam families not currently annotated as related in Pfam. We find that HMMER3 E-value estimates seem to be less accurate for families that feature periodic patterns of compositional bias, such as the ones typically observed in coiled-coils. These results support the continued use of manually curated inclusion thresholds in the Pfam database, especially on the subset of families that have been identified as problematic in experiments such as these. They also highlight the need for developing new methods that can correct for this particular type of compositional bias.</p>
},
	issn = {1362-4962},
	doi = {10.1093/nar/gkt263},
	author = {Mistry, Jaina and Finn, Robert D and Eddy, Sean R. and Bateman, Alex and Punta, Marco}
}
@article {6296,
	title = {The Pfam protein families database.},
	journal = {Nucleic acids research},
	volume = {40},
	year = {2012},
	month = {2012 Jan},
	pages = {D290-301},
	abstract = {<p>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 {\textquoteright}sunburst{\textquoteright} 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.</p>
},
	keywords = {Amino Acid, Databases, Encyclopedias as Topic, Internet, Protein, Protein Structure, Proteins, Sequence Homology, Tertiary},
	issn = {1362-4962},
	doi = {10.1093/nar/gkr1065},
	author = {Punta, Marco and Coggill, Penny C and Eberhardt, Ruth Y and Mistry, Jaina and Tate, John and Boursnell, Chris and Pang, Ningze and Forslund, Kristoffer and Ceric, Goran and Clements, Jody and Heger, Andreas and Holm, Liisa and Sonnhammer, Erik L L and Sean R. Eddy and Bateman, Alex and Finn, Robert D}
}
