OrthoDB v9.1: Cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

Nucleic Acids Research

Volumn 45, Issue D1, 2017, Pages D744-D749

  Zdobnov, Evgeny M ^a,b   Tegenfeldt, Fredrik ^a,b   Kuznetsov, Dmitry ^a,b   Waterhouse, Robert M ^a,b   Simao, Felipe A ^a,b   Ioannidis, Panagiotis ^a,b   Seppey, Mathieu ^a,b   Loetscher, Alexis ^a,b   Kriventseva, Evgenia V ^a,b  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BACTERIAL GENETICS; CLADISTICS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER INTERFACE; EVOLUTIONARY HOMOLOGY; GENE FUNCTION; GENE MAPPING; MOLECULAR GENETICS; NONHUMAN; ORTHOLOGY; PHYLOGENY; PREDICTOR VARIABLE; SEQUENCE HOMOLOGY; SOFTWARE; ARCHAEON; BACTERIUM; BIOLOGY; FUNGUS; GENETIC DATABASE; GENETICS; GENOMICS; MOLECULAR EVOLUTION; PLANT; PROCEDURES; VIRUS; WEB BROWSER;

ALGORITHMS; ANIMALS; ARCHAEA; BACTERIA; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; FUNGI; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; PLANTS; SOFTWARE; USER-COMPUTER INTERFACE; VIRUSES; WEB BROWSER;

EID: 85016153856     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1119     Document Type: Article

References (34)

1. Koonin, E.V. (2005) Orthologs, paralogs and evolutionary genomics. Annu. Rev. Genet., 39, 309-338.
2. Gabaldon, T. and Koonin, E.V. (2013) Functional and evolutionary implications of gene orthology. Nat. Rev. Genet., 14, 360-366.
3. Tatusov, R.L., Galperin, M.Y., Natale, D.A. and Koonin, E.V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28, 33-36.
4. Sonnhammer, E.L., Gabaldon, T., Sousa da Silva, A.W., Martin, M., Robinson-Rechavi, M., Boeckmann, B., Thomas, P.D., Dessimoz, C. and Quest for Orthologs consortium. (2014) Big data and other challenges in the quest for orthologs. Bioinformatics, 30, 2993-2998.
5. Kriventseva, E.V., Rahman, N., Espinosa, O. and Zdobnov, E.M. (2008) OrthoDB: the hierarchical catalog of eukaryotic orthologs. Nucleic Acids Res., 36, D271-275.
6. Bovine Genome, S., Analysis, C., Elsik, C.G., Tellam, R.L., Worley, K.C., Gibbs, R.A., Muzny, D.M., Weinstock, G.M., Adelson, D.L., Eichler, E.E. et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science, 324, 522-528.
7. Tribolium Genome Sequencing, C., Richards, S., Gibbs, R.A., Weinstock, G.M., Brown, S.J., Denell, R., Beeman, R.W., Gibbs, R., Beeman, R.W., Brown, S.J. et al. (2008) The genome of the model beetle and pest Tribolium castaneum. Nature, 452, 949-955.
8. Waterhouse, R.M., Kriventseva, E.V., Meister, S., Xi, Z., Alvarez, K.S., Bartholomay, L.C., Barillas-Mury, C., Bian, G., Blandin, S., Christensen, B.M. et al. (2007) Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes. Science, 316, 1738-1743.
9. Nene, V., Wortman, J.R., Lawson, D., Haas, B., Kodira, C., Tu, Z.J., Loftus, B., Xi, Z., Megy, K., Grabherr, M. et al. (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science, 316, 1718-1723.
10. Honeybee Genome Sequencing, C. (2006) Insights into social insects from the genome of the honeybee Apis mellifera. Nature, 443, 931-949.
11. Kriventseva, E.V., Tegenfeldt, F., Petty, T.J., Waterhouse, R.M., Simao, F.A., Pozdnyakov, I.A., Ioannidis, P. and Zdobnov, E.M. (2015) OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res., 43, D250-D256.
12. Federhen, S. (2012) The NCBI Taxonomy database. Nucleic Acids Res., 40, D136-D143.
13. Yates, A., Akanni, W., Amode, M.R., Barrell, D., Billis, K., Carvalho-Silva, D., Cummins, C., Clapham, P., Fitzgerald, S., Gil, L. et al. (2016) Ensembl 2016. Nucleic Acids Res., 44, D710-D716.
14. Legeai, F., Shigenobu, S., Gauthier, J.P., Colbourne, J., Rispe, C., Collin, O., Richards, S., Wilson, A.C., Murphy, T. and Tagu, D. (2010) AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. Insect. Mol. Biol., 19(Suppl 2), 5-12.
15. Kim, H.S., Murphy, T., Xia, J., Caragea, D., Park, Y., Beeman, R.W., Lorenzen, M.D., Butcher, S., Manak, J.R. and Brown, S.J. (2010) BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Nucleic Acids Res., 38, D437-D442.
16. Tang, W., Yu, L., He, W., Yang, G., Ke, F., Baxter, S.W., You, S., Douglas, C.J. and You, M. (2014) DBM-DB: the diamondback moth genome database. Database (Oxford), 2014, doi:10.1093/database/bat087.
17. Millburn, G.H., Crosby, M.A., Gramates, L.S., Tweedie, S. and FlyBase, C. (2016) FlyBase portals to human disease research using Drosophila models. Dis. Model. Mech., 9, 245-252.
18. Elsik, C.G., Tayal, A., Diesh, C.M., Unni, D.R., Emery, M.L., Nguyen, H.N. and Hagen, D.E. (2016) Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. Nucleic Acids Res., 44, D793-D800.
19. Brown, G.R., Hem, V., Katz, K.S., Ovetsky, M., Wallin, C., Ermolaeva, O., Tolstoy, I., Tatusova, T., Pruitt, K.D., Maglott, D.R. et al. (2015) Gene: a gene-centered information resource at NCBI. Nucleic Acids Res., 43, D36-D42.
20. Duan, J., Li, R., Cheng, D., Fan, W., Zha, X., Cheng, T., Wu, Y., Wang, J., Mita, K., Xiang, Z. et al. (2010) SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology. Nucleic Acids Res., 38, D453-D456.
21. Giraldo-Calderon, G.I., Emrich, S.J., MacCallum, R.M., Maslen, G., Dialynas, E., Topalis, P., Ho, N., Gesing, S., VectorBase, C., Madey, G. et al. (2015) VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res., 43, D707-D713.
22. Colbourne, J.K., Singan, V.R. and Gilbert, D.G. (2005) wFleaBase: the Daphnia genome database. BMC Bioinform., 6, doi:10.1186/1471-2105-6-45.
23. i5K Consortium (2013) The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture and the environment. J. Hered., 104, 595-600.
24. Nordberg, H., Cantor, M., Dusheyko, S., Hua, S., Poliakov, A., Shabalov, I., Smirnova, T., Grigoriev, I.V. and Dubchak, I. (2014) The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res., 42, D26-D31.
25. UniProt, C. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
26. Kersey, P.J., Allen, J.E., Armean, I., Boddu, S., Bolt, B.J., Carvalho-Silva, D., Christensen, M., Davis, P., Falin, L.J., Grabmueller, C. et al. (2016) Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res., 44, D574-D580.
27. Simao, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V. and Zdobnov, E.M. (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210-3212.
28. Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B. et al. (2013) Metagenomic species profling using universal phylogenetic marker genes. Nat. Methods, 10, 1196-1199.
29. Howe, K.L., Bolt, B.J., Cain, S., Chan, J., Chen, W.J., Davis, P., Done, J., Down, T., Gao, S., Grove, C. et al. (2016) WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res., 44, D774-D780.
30. Ruzicka, L., Bradford, Y.M., Frazer, K., Howe, D.G., Paddock, H., Ramachandran, S., Singer, A., Toro, S., Van Slyke, C.E., Eagle, A.E. et al. (2015) ZFIN, The zebrafsh model organism database: Updates and new directions. Genesis, 53, 498-509.
31. Bult, C.J., Eppig, J.T., Blake, J.A., Kadin, J.A., Richardson, J.E. and Mouse Genome Database, G. (2016) Mouse genome database 2016. Nucleic Acids Res., 44, D840-D847.
32. Cherry, J.M. (2015) The Saccharomyces Genome Database: gene product annotation of function, process and component. Cold Spring Harb. Protoc., 12, doi:10.1101/pdb.prot088914.
33. Gao, F., Luo, H., Zhang, C.T. and Zhang, R. (2015) Gene essentiality analysis based on DEG 10, an updated database of essential genes. Methods Mol. Biol., 1279, 219-233.
34. Waterhouse, R.M., Zdobnov, E.M. and Kriventseva, E.V. (2011) Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods and fungi. Genome Biol. Evol., 3, 75-86.