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. 2012 Jan;40(Database issue):D306-12.
doi: 10.1093/nar/gkr948. Epub 2011 Nov 16.

InterPro in 2011: New Developments in the Family and Domain Prediction Database

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Free PMC article

InterPro in 2011: New Developments in the Family and Domain Prediction Database

Sarah Hunter et al. Nucleic Acids Res. .
Free PMC article

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

Figures

Figure 1.
Figure 1.
The ‘Overview' page on the new set of InterPro entry pages, including the family hierarchy for this entry, an extensive description of the family and cross references to three GO terms that are associated with this family. In this case, the entry comprises a single integrated PRINTS signature. Note the red 'F' icon that indicates that this entry describes a protein family.
Figure 2.
Figure 2.
The InterPro BioMart. This example illustrates the use of the BioMart to return a large set of data. In this case, a query has been built to return all proteins that are predicted to be members of the rhodopsin-like GPCRs (IPR000276) in Drosophila melanogaster.

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References

    1. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res. 2010;38:D211–D22. - PMC - PubMed
    1. Attwood TK, Bradley P, Flower DR, Gaulton A, Maudling N, Mitchell AL, Moulton G, Nordle A, Paine K, Taylor P, et al. PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res. 2003;31:400–402. - PMC - PubMed
    1. Sigrist CJA, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 2010;38:D161–D166. - PMC - PubMed
    1. Letunic I, Doerks T, Bork P. SMART 6: recent updates and new developments. Nucleic Acids Res. 2009;37:D229–D232. - PMC - PubMed
    1. Bru C, Courcelle E, Carrère S, Beausse Y, Dalmar S, Kahn D. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 2005;33:D212–D215. - PMC - PubMed

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