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      InterPro, progress and status in 2005

      research-article
      1 , 1 , 3 ,   4 , 2 , 1 , 1 , 3 , 5 , 6 , 6 , 7 , 8 , 1 , 2 , 1 , 9 , 10 , 1 , 4 , 8 , 1 , 1 , 1 , 1 , 5 , 11 , 1 , 1 , 1 , 3 , 12 , 1 , 6 , 13 , 1 , 10 , 4 , 1 , 2 , 1 , 12
      Nucleic Acids Research
      Oxford University Press
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          Abstract

          InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver ( http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

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          Most cited references8

          • Record: found
          • Abstract: found
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          The TIGRFAMs database of protein families.

          TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature references and pointers to related TIGRFAMs, Pfam and InterPro models. These models are designed to support both automated and manually curated annotation of genomes. TIGRFAMs contains models of full-length proteins and shorter regions at the levels of superfamilies, subfamilies and equivalogs, where equivalogs are sets of homologous proteins conserved with respect to function since their last common ancestor. The scope of each model is set by raising or lowering cutoff scores and choosing members of the seed alignment to group proteins sharing specific function (equivalog) or more general properties. The overall goal is to provide information with maximum utility for the annotation process. TIGRFAMs is thus complementary to Pfam, whose models typically achieve broad coverage across distant homologs but end at the boundaries of conserved structural domains. The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs.
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            • Record: found
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            The PROSITE database, its status in 2002.

            PROSITE [Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583-3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215-219] is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http://www.expasy.org/prosite/) consists of biologically significant patterns and profiles designed in such a way that with appropriate computational tools it can rapidly and reliably help to determine to which known family of proteins (if any) a new sequence belongs, or which known domain(s) it contains.
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              • Record: found
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              PRINTS and its automatic supplement, prePRINTS.

              The PRINTS database houses a collection of protein fingerprints. These may be used to assign uncharacterised sequences to known families and hence to infer tentative functions. The September 2002 release (version 36.0) includes 1800 fingerprints, encoding approximately 11 000 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. In addition to its continued steady growth, we report here the development of an automatic supplement, prePRINTS, designed to increase the coverage of the resource and reduce some of the manual burdens inherent in its maintenance. The databases are accessible for interrogation and searching at http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                1 January 2005
                17 December 2004
                : 33
                : Database Issue
                : D201-D205
                Affiliations
                [1 ]EMBL Outstation—European Bioinformatics Institute and [2 ]Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, [3 ]School of Biological Sciences and Department of Computer Science, The University of Manchester, Manchester, UK, [4 ]Swiss Institute for Bioinformatics, Geneva, Switzerland, [5 ]Biocomputing Unit EMBL, Heidelberg, Germany, [6 ]Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland, [7 ]Wellcome Trust Centre for Human Genetics, Oxford, UK, [8 ]CNRS/INRA, Toulouse, France, [9 ]Genomic Sciences Centre, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan, [10 ]The Institute for Genomic Research, MD, USA, [11 ]MRC Laboratory of Molecular Biology, Cambridge, UK, [12 ]Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA and [13 ]MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, UK
                Author notes
                [*]

                To whom correspondence should be addressed. Tel: +44 0 1223 494 602; Fax: +44 0 1223 494 468; Email: mulder@ 123456ebi.ac.uk

                [a]

                The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@ 123456oupjournals.org .

                [a]

                © 2005, the authors

                Article
                gki106
                10.1093/nar/gki106
                540060
                15608177
                21574065-f883-4fff-b98b-cfbe24b258a2
                Copyright © 2005 Oxford University Press
                History
                : 20 September 2004
                : 18 October 2004
                : 18 October 2004
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                Genetics
                Genetics

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