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Interpro: the Integrative Protein Signature Database InterPro: the integrative protein signature database Sarah Hunter, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, et al. To cite this version: Sarah Hunter, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Alex Bateman, et al.. InterPro: the integrative protein signature database. Nucleic Acids Research, Oxford University Press, 2009, 37 (Database issue), pp.D211-D215. 10.1093/nar/gkn785. hal-01214141 HAL Id: hal-01214141 https://hal.archives-ouvertes.fr/hal-01214141 Submitted on 9 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Published online 21 October 2008 Nucleic Acids Research, 2009, Vol. 37, Database issue D211–D215 doi:10.1093/nar/gkn785 InterPro: the integrative protein signature database Sarah Hunter1,*, Rolf Apweiler1, Teresa K. Attwood2, Amos Bairoch3, Alex Bateman4, David Binns1, Peer Bork5, Ujjwal Das1, Louise Daugherty1, Lauranne Duquenne6, Robert D. Finn4, Julian Gough7, Daniel Haft8, Nicolas Hulo3, Daniel Kahn6, Elizabeth Kelly9, Aure´ lie Laugraud6, Ivica Letunic5, David Lonsdale1, Rodrigo Lopez1, Martin Madera7, John Maslen1, Craig McAnulla1, Jennifer McDowall1, Jaina Mistry4, Downloaded from Alex Mitchell1,2, Nicola Mulder9, Darren Natale10, Christine Orengo11, Antony F. Quinn1, Jeremy D. Selengut8, Christian J. A. Sigrist3, Manjula Thimma1, Paul D. Thomas12, Franck Valentin1, Derek Wilson13, 10 11 Cathy H. Wu and Corin Yeats http://nar.oxfordjournals.org/ 1EMBL Outstation European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, 2Faculty of Life Science and School of Computer Science, The University of Manchester, Manchester, UK, 3Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland, 4The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 5European Molecular Laboratory (EMBL), Heidelberg, Germany, 6Pole Rhone-Alpins de BioInformatique (PRABI) and Laboratoire de Biome´ trie et Biologie Evolutive, CNRS, INRIA, Universite´ de Lyon, Universite´ Lyon 1, Villeurbanne, France, 7Department of Computer Science, 8 University of Bristol, Woodland Road, Bristol, UK, J. Craig Venter Institute (JCVI), Rockville, MD, 20850, USA, at INRA Institut National de la Recherche Agronomique on October 9, 2015 9Computational Biology Unit, University of Cape Town, South Africa, 10Protein Information Resource (PIR), Georgetown University Medical Center, Washington, DC, USA, 11Department of Structural and Molecular Biology, University College London, London, UK, 12Evolutionary Systems Biology, SRI International, Menlo Park, CA, 94025-3493, USA and 13MRC Laboratory of Molecular Biology, Cambridge Received September 15, 2008; Revised October 8, 2008; Accepted October 9, 2008 ABSTRACT predicted protein–protein interaction database and The InterPro database (http://www.ebi.ac.uk/inter the SPICE and Dasty viewers. The latest public pro/) integrates together predictive models or ‘sig- release (v18.0) covers 79.8% of UniProtKB (v14.1) natures’ representing protein domains, families and and consists of 16 549 entries. InterPro data may functional sites from multiple, diverse source data- be accessed either via the web address above, via bases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, web services, by downloading files by anonymous ProDom, PROSITE, SMART, SUPERFAMILY and FTP or by using the InterProScan search software TIGRFAMs. Integration is performed manually and (http://www.ebi.ac.uk/Tools/InterProScan/). approximately half of the total ~58 000 signatures available in the source databases belong to an INTRODUCTION InterPro entry. Recently, we have started to also InterPro (1) is an integrative database which was founded display the remaining un-integrated signatures via 10 years ago when the PROSITE (2), PRINTS (3), Pfam (4) our web interface. Other developments include the and ProDom (5) databases formed a consortium to amal- provision of non-signature data, such as structural gamate the predictive signatures they individually pro- data, in new XML files on our FTP site, as well as duced into a single resource. Since then, six other member the inclusion of matchless UniProtKB proteins in databases have also joined and their data has been the existing match XML files. The web interface integrated: SMART (6), TIGRFAMs (7), PIRSF (8), has been extended and now links out to the ADAN SUPERFAMILY (9), PANTHER (10) and Gene3D (11). *To whom correspondence should be addressed. Tel: +44 0 1223 494 481; Fax: +44 0 1223 494 468; Email: [email protected] ß 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. D212 Nucleic Acids Research, 2009, Vol. 37, Database issue The signatures of each member database are built using PDB (21). Additionally, if a protein has a solved 3D different but complementary methodologies. structure in PDB or a structure modelled in either the When different signatures match the same set of proteins MODBASE (22) or SWISS-MODEL (23) databases, this in the same region on the sequence, they are presumed to information is shown together with the member databases’ be describing the same functional family, domain or site signature matches in the graphical display on the InterPro and are placed into a single InterPro entry by a curator. Web interface. Grouping equivalent signatures from different sources Users are able to access all pre-computed matches of together in this way has obvious benefits, giving signatures signatures to UniProtKB via the web interface in a variety consistent names and annotation. It also highlights poten- of graphical and text-based formats. They can change how tially erroneous signature hits. One would expect that these matches are shown by either sorting by UniProtKB remote homologues might only match a single signature identifier or name, for example, or by electing to display from a multiple signature entry but these outliers could matches based on their taxonomy, solved 3D structures or Downloaded from also be explained by single matches being false positive, splice variants. They can also download XML-format files hence the user should regard these results more cautiously. of matches to UniProtKB, the UniProt Archive (UniParc) Collectively considering the total set of signatures from and UniMES meta-genomic sequence database. the member databases also increases overall coverage of InterProScan is made available via the web at http:// protein space. The coverage of various sequence data- www.ebi.ac.uk/Tools/InterProScan/, and the entire pack- http://nar.oxfordjournals.org/ bases by InterPro signatures is shown in Table 1. InterPro age can be downloaded from the FTP site ftp://ftp.ebi.ac. signature matches to the UniProt Knowledgebase [Uni- uk/pub/software/unix/iprscan/index.html. InterProScan ProtKB; (12)] are regularly calculated using the Inter- allows users to submit their own sequences to the search ProScan software package (13) and this information is algorithms and processing from InterPro and its member used to aid UniProtKB curators in their annotation of databases. They can receive results in various formats Swiss-Prot proteins, as well as being the basis of the showing the signatures that match their sequence(s), the InterPro entry (if any) into which each signature is inte- automatic systems which add annotation to UniProtKB/ grated and any GO terms associated with those entries. TrEMBL (12). The UniParc protein archive and UniMES at INRA Institut National de la Recherche Agronomique on October 9, 2015 SOAP-based web services also exist (http://www.ebi.ac. meta-genomic sequence databases (14) are also put uk/Tools/webservices/WSInterProScan.html) which allow through InterPro analysis pipelines and many genomic users to submit their own nucleotide and protein sequencing projects continue to use InterPro and its soft- sequences programmatically (24). ware to functionally characterize whole genomes (15,16). If a signature only matches a subset of proteins com- pared to another signature, it is likely that this signature NEW FEATURES IN InterPro is more functionally or taxonomically specific than the Annotation other. In this case, the signatures would be deemed to be related; the signature matching the subset would be InterPro curators continue to integrate new signatures termed a child, the other signature being its parent. from member databases into entries. The entries are These parent–child relationships are created by InterPro’s classified according to the type of signature they group curators during the integration process and a hierarchy together. Previously, the categories comprised family, of how the integrated signatures relate to each other is domain, repeat, post-translational modification (PTM), thus constructed. In this way, InterPro also increases the active
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