InterProScan 5: Genome-scale Protein Function Classification

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2014 Jan 24

PMID 24451626

Citations 4039

Authors

Philip Jones

David Binns

Hsin-Yu Chang

Matthew Fraser

Weizhong Li

Craig McAnulla

Hamish McWilliam

John Maslen

Alex Mitchell

Gift Nuka

Sebastien Pesseat

Antony F Quinn

Amaia Sangrador-Vegas

Maxim Scheremetjew

Siew-Yit Yong

Rodrigo Lopez

Sarah Hunter

Affiliations

Soon will be listed here.

Abstract

Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code.

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References

Letunic I, Doerks T, Bork P . SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 2011; 40(Database issue):D302-5. PMC: 3245027. DOI: 10.1093/nar/gkr931. View

Wu C, Nikolskaya A, Huang H, Yeh L, Natale D, Vinayaka C . PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 2003; 32(Database issue):D112-4. PMC: 308831. DOI: 10.1093/nar/gkh097. View

Petersen T, Brunak S, von Heijne G, Nielsen H . SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011; 8(10):785-6. DOI: 10.1038/nmeth.1701. View

Eddy S . A new generation of homology search tools based on probabilistic inference. Genome Inform. 2010; 23(1):205-11. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S, Kahn D . The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 2004; 33(Database issue):D212-5. PMC: 539988. DOI: 10.1093/nar/gki034. View

Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J . A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 2010; 38(Web Server issue):W695-9. PMC: 2896090. DOI: 10.1093/nar/gkq313. View

Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R . InterProScan: protein domains identifier. Nucleic Acids Res. 2005; 33(Web Server issue):W116-20. PMC: 1160203. DOI: 10.1093/nar/gki442. View

Attwood T, Coletta A, Muirhead G, Pavlopoulou A, Philippou P, Popov I . The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012. Database (Oxford). 2012; 2012:bas019. PMC: 3326521. DOI: 10.1093/database/bas019. View

10.

Bairoch A . The ENZYME database in 2000. Nucleic Acids Res. 1999; 28(1):304-5. PMC: 102465. DOI: 10.1093/nar/28.1.304. View

11.

Sigrist C, de Castro E, Cerutti L, Cuche B, Hulo N, Bridge A . New and continuing developments at PROSITE. Nucleic Acids Res. 2012; 41(Database issue):D344-7. PMC: 3531220. DOI: 10.1093/nar/gks1067. View

12.

Kall L, Krogh A, Sonnhammer E . A combined transmembrane topology and signal peptide prediction method. J Mol Biol. 2004; 338(5):1027-36. DOI: 10.1016/j.jmb.2004.03.016. View

13.

Mi H, Muruganujan A, Thomas P . PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2012; 41(Database issue):D377-86. PMC: 3531194. DOI: 10.1093/nar/gks1118. View

14.

Kanehisa M . Molecular network analysis of diseases and drugs in KEGG. Methods Mol Biol. 2012; 939:263-75. DOI: 10.1007/978-1-62703-107-3_17. View

15.

Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E . The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet. 2011; 7(2):e1002007. PMC: 3037820. DOI: 10.1371/journal.pgen.1002007. View

16.

Haft D, Selengut J, Richter R, Harkins D, Basu M, Beck E . TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res. 2012; 41(Database issue):D387-95. PMC: 3531188. DOI: 10.1093/nar/gks1234. View

17.

Pedruzzi I, Rivoire C, Auchincloss A, Coudert E, Keller G, de Castro E . HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 2012; 41(Database issue):D584-9. PMC: 3531088. DOI: 10.1093/nar/gks1157. View

18.

. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2011; 40(Database issue):D71-5. PMC: 3245120. DOI: 10.1093/nar/gkr981. View

19.

KROGH A, Larsson B, von Heijne G, Sonnhammer E . Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001; 305(3):567-80. DOI: 10.1006/jmbi.2000.4315. View

20.

Punta M, Coggill P, Eberhardt R, Mistry J, Tate J, Boursnell C . The Pfam protein families database. Nucleic Acids Res. 2011; 40(Database issue):D290-301. PMC: 3245129. DOI: 10.1093/nar/gkr1065. View