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

Alex L Mitchell; Teresa K Attwood; Patricia C Babbitt; Matthias Blum; Peer Bork; Alan Bridge; Shoshana D Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew I Fraser; Julian Gough; David R Haft; Hongzhan Huang; Ivica Letunic; Rodrigo Lopez; Aurélien Luciani; Fabio Madeira; Aron Marchler-Bauer; Huaiyu Mi; Darren A Natale; Marco Necci; Gift Nuka; Christine Orengo; Arun P Pandurangan; Typhaine Paysan-Lafosse; Sebastien Pesseat; Simon C Potter; Matloob A Qureshi; Neil D Rawlings; Nicole Redaschi; Lorna J Richardson; Catherine Rivoire; Gustavo A Salazar; Amaia Sangrador-Vegas; Christian J A Sigrist; Ian Sillitoe; Granger G Sutton; Narmada Thanki; Paul D Thomas; Silvio C E Tosatto; Siew-Yit Yong; Robert D Finn

doi:10.1093/nar/gky1100

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

Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360. doi: 10.1093/nar/gky1100.

Authors

Alex L Mitchell¹, Teresa K Attwood², Patricia C Babbitt³, Matthias Blum¹, Peer Bork⁴, Alan Bridge⁵, Shoshana D Brown³, Hsin-Yu Chang¹, Sara El-Gebali¹, Matthew I Fraser¹, Julian Gough⁶, David R Haft⁷, Hongzhan Huang⁸, Ivica Letunic⁹, Rodrigo Lopez¹, Aurélien Luciani¹, Fabio Madeira¹, Aron Marchler-Bauer¹⁰, Huaiyu Mi¹¹, Darren A Natale¹², Marco Necci^{13

14

15}, Gift Nuka¹, Christine Orengo¹⁶, Arun P Pandurangan⁶, Typhaine Paysan-Lafosse¹, Sebastien Pesseat¹, Simon C Potter¹, Matloob A Qureshi¹, Neil D Rawlings¹, Nicole Redaschi⁵, Lorna J Richardson¹, Catherine Rivoire⁵, Gustavo A Salazar¹, Amaia Sangrador-Vegas¹, Christian J A Sigrist⁵, Ian Sillitoe¹⁶, Granger G Sutton⁷, Narmada Thanki¹⁰, Paul D Thomas¹¹, Silvio C E Tosatto¹³, Siew-Yit Yong¹, Robert D Finn¹

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
² School of Computer Science, The University of Manchester, Manchester M13 9PL, UK.
³ Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.
⁴ European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr.1, 69117 Heidelberg, Germany.
⁵ Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland.
⁶ Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
⁷ J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA.
⁸ Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
⁹ Biobyte Solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany.
¹⁰ National Center for Biotechnology Information, National Library of Medicine, NIH Bldg, 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.
¹¹ Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA.
¹² Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA.
¹³ Department of Biomedical Sciences, University of Padua, via U. Bassi 58/b, 35131 Padua, Italy.
¹⁴ Department of Agricultural Sciences, University of Udine, via Palladio 8, 33100 Udine, Italy.
¹⁵ Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Italy.
¹⁶ Structural and Molecular Biology, University College London, Darwin Building, London WC1E 6BT, UK.

Abstract

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.

Publication types

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

MeSH terms

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

Abstract

Publication types

MeSH terms

Grants and funding