InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Animals Databases, Genetic Databases, Protein Gene Ontology Humans Internet Molecular Sequence Annotation Multigene Family Protein Domains / genetics Sequence Homology, Amino Acid Software User-Computer Interface

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
08 01 2019
Historique:
received: 27 09 2018
accepted: 22 10 2018
pubmed: 7 11 2018
medline: 14 5 2020
entrez: 7 11 2018
Statut: ppublish

Résumé

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.

Identifiants

DOI: 10.1093/nar/gky1100 PMID: 30398656 PMC: PMC6323941
pubmed: 30398656
pii: 5162469
doi: 10.1093/nar/gky1100
pmc: PMC6323941
doi:

Types de publication

Journal Article Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

D351-D360

Subventions

Organisme : NHGRI NIH HHS
ID : U41 HG002273
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N019172/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/L024136/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N00521X/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UP_1201/14
Pays : United Kingdom

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Auteurs

Alex L Mitchell (AL)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Teresa K Attwood (TK)

School of Computer Science, The University of Manchester, Manchester M13 9PL, UK.

Patricia C Babbitt (PC)

Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.

Matthias Blum (M)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Peer Bork (P)

European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr.1, 69117 Heidelberg, Germany.

Alan Bridge (A)

Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.

Shoshana D Brown (SD)

Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.

Hsin-Yu Chang (HY)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Sara El-Gebali (S)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Matthew I Fraser (MI)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Julian Gough (J)

Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.

David R Haft (DR)

J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA.

Hongzhan Huang (H)

Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.

Ivica Letunic (I)

Biobyte Solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany.

Rodrigo Lopez (R)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Aurélien Luciani (A)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Fabio Madeira (F)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Aron Marchler-Bauer (A)

National Center for Biotechnology Information, National Library of Medicine, NIH Bldg, 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.

Huaiyu Mi (H)

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.

Darren A Natale (DA)

Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA.

Marco Necci (M)

Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.
Department of Agricultural Sciences, University of Udine, via Palladio 8, 33100 Udine, Italy.
Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Italy.

Gift Nuka (G)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Christine Orengo (C)

Structural and Molecular Biology, University College London, Darwin Building, London WC1E 6BT, UK.

Arun P Pandurangan (AP)

Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.

Typhaine Paysan-Lafosse (T)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Sebastien Pesseat (S)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Simon C Potter (SC)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Matloob A Qureshi (MA)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Neil D Rawlings (ND)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Nicole Redaschi (N)

Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.

Lorna J Richardson (LJ)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Catherine Rivoire (C)

Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.

Gustavo A Salazar (GA)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Amaia Sangrador-Vegas (A)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Christian J A Sigrist (CJA)

Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.

Ian Sillitoe (I)

Structural and Molecular Biology, University College London, Darwin Building, London WC1E 6BT, UK.

Granger G Sutton (GG)

J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA.

Narmada Thanki (N)

National Center for Biotechnology Information, National Library of Medicine, NIH Bldg, 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.

Paul D Thomas (PD)

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.

Silvio C E Tosatto (SCE)

Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.

Siew-Yit Yong (SY)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Robert D Finn (RD)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Bases de données de protéines › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Vocabulaire contrôlé › Ontologies biologiques › Gene Ontology › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Systèmes informatiques › Réseaux de communication entre ordinateurs › Internet › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Famille multigénique › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Structure tertiaire des protéines › Domaines protéiques › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Phénomènes génétiques › Similitude de séquences › Similitude de séquences d'acides aminés › InterPro in 2019: improving coverage,...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › InterPro in 2019: improving coverage,...
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