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112 Janelia Publications

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    01/01/12 | The Pfam protein families database.
    Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Sean R. Eddy , Bateman A, Finn RD
    Nucleic acids research. 2012 Jan;40:D290-301. doi: 10.1093/nar/gkr1065

    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.

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    01/01/12 | Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.
    Brody T, Yavatkar AS, Kuzin A, Kundu M, Tyson LJ, Ross J, Lin T, Lee C, Awasaki T, Lee T, Odenwald WF
    Developmental Dynamics: An Official Publication of the American Association of Anatomists. 2012 Jan;241:169-89. doi: 10.1002/dvdy.22728

    Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs.

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