Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

Molecular Biology and Evolution

Volumn 34, Issue 8, 2017, Pages 2115-2122

  Huerta Cepas, Jaime ^a   Forslund, Kristoffer ^a   Coelho, Luis Pedro ^a   Szklarczyk, Damian ^b,c   Jensen, Lars Juhl ^d   Von Mering, Christian ^b,c   Bork, Peer ^a,e,f,g  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d University of Copenhagen   (Denmark)

^e UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^f MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^g UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

Comparative genomics; Functional annotation; Gene function; Genomics; Metagenomics; Orthology

Indexed keywords

ALGORITHM; COMPUTER SIMULATION; GENE ONTOLOGY; GENETIC DATABASE; GENETICS; GENOME; PHYLOGENY; PROCEDURES; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SOFTWARE; STATISTICS AND NUMERICAL DATA;

ALGORITHMS; COMPUTER SIMULATION; DATABASES, GENETIC; DATABASES, PROTEIN; GENE ONTOLOGY; GENOME; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 85028399845     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msx148     Document Type: Article

References (22)

1. Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, et al. 2016. Standardized benchmarking in the quest for orthologs. Nat Methods. 13:425-430.
2. Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 12:59-60.
3. Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P,McAnulla C, Mitchell A, Sangrador-Vegas A, Yong S-Y, Mulder N, Hunter S. 2012. Manual GO annotation of predictive protein signatures: The InterPro approach to GO curation. Database 2012:bar068.
4. Deegan née Clark JI, Dimmer EC, Mungall CJ. 2010. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics. 11:530.
5. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol. 7:e1002195.
6. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, et al. 2014. Pfam: The protein families database. Nucleic Acids Res. 42:D222-D230.
7. Fitch WM. 1970. Distinguishing homologous from analogous proteins. Syst Zool. 19:99-113.
8. Gabaldon T, Koonin EV. 2013. Functional and evolutionary implications of gene orthology. Nat Rev Genet. 14:360-366.
9. Galperin MY, Makarova KS,Wolf YI, Koonin EV. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43:D261-D269.
10. Gene Ontology Consortium. 2015. Gene Ontology Consortium: going forward. Nucleic Acids Res. 43:D1049-D1056.
11. Götz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A. 2008. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 36:3420-3435.
12. Huerta-Cepas J, Serra F, Bork P. 2016. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol Biol Evol. 33:1635-1638.
13. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, MendeDR, Sunagawa S, KuhnM, et al. 2016. eggNOG4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44:D286-D293.
14. Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, et al. 2016. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 17:184.
15. Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, et al. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236-1240.
16. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42:D199-D205.
17. Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. 2016. MOCAT2: A metagenomic assembly, annotation and profiling framework. Bioinformatics 32:2520-2523.
18. Mende DR, Sunagawa S, Zeller G, Bork P. 2013. Accurate and universal delineation of prokaryotic species. Nat Methods. 10:881-884.
19. Mende DR, Waller AS, Sunagawa S, Jarvelin AI, Chan MM, Arumugam M, Raes J, Bork P. 2012. Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS ONE. 7:e31386.
20. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, et al. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42:D206-D214.
21. Söding J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960.
22. Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-637.