OrthoVenn: A web server for genome wide comparison and annotation of orthologous clusters across multiple species

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W78-W84

  Wang, Yi ^a,b,c   Coleman Derr, Devin ^d   Chen, Guoping ^c   Gu, Yong Q ^a  

^a WESTERN REGIONAL RESEARCH CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c CHONGQING UNIVERSITY   (China)

^d PLANT GENE EXPRESSION CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AEGILOPS TAUSCHII; AMINO ACID SEQUENCE; ARTICLE; BARLEY; BRACHYPODIUM; CONTROLLED STUDY; GENE CLUSTER; GENE DOSAGE; GENETIC PROCEDURES; GENOME WIDE COMPARISON; MAIZE; NONHUMAN; ORTHOLOGOUS CLUSTER; POACEAE; PRIORITY JOURNAL; RICE; SEQUENCE ANALYSIS; SORGHUM; SPECIES IDENTIFICATION; ANIMAL; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENOMICS; INTERNET; MOLECULAR GENETICS; MULTIGENE FAMILY; PHYLOGENY; PLANT GENOME;

ANIMALS; CLUSTER ANALYSIS; GENOME, PLANT; GENOMICS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84979865099     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv487     Document Type: Article

References (35)

1. Fitch, W.M. (1970) Distinguishing homologous from analogous proteins. Syst. Zool., 19, 99-113.
2. Henikoff, S., Greene, E.A., Pietrokovski, S., Bork, P., Attwood, T.K. and Hood, L. (1997) Gene families: the taxonomy of protein paralogs and chimeras. Science, 278, 609-614.
3. Mushegian, A.R., Garey, J.R., Martin, J. and Liu, L.X. (1998) Large-scale taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes. Genome Res., 8, 590-598.
4. Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldon, T., Rattei, T., Creevey, C., Kuhn, M. et al. (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res., 42, D231-D239.
5. Sonnhammer, E.L. and Ostlund, G. (2015) In Paranoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Res., 43, D234-D239.
6. 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.
7. Pryszcz, L.P., Huerta-Cepas, J. and Gabaldon, T. (2011) MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res., 39, e32.
8. Huerta-Cepas, J., Capella-Gutierrez, S., Pryszcz, L.P., Marcet-Houben, M. and Gabaldon, T. (2014) PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res., 42, D897-D902.
9. Altenhoff, A.M. and Dessimoz, C. (2012) Inferring orthology and paralogy. Methods Mol. Biol., 855, 259-279.
10. Argout, X., Salse, J., Aury, J.M., Guiltinan, M.J., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S.N. et al. (2011) The genome of Theobroma cacao. Nat. Genet., 43, 101-108.
11. D'Hont, A., Denoeud, F., Aury, J.M., Baurens, F.C., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M. et al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488, 213-217.
12. Cho, Y.S., Hu, L., Hou, H., Lee, H., Xu, J., Kwon, S., Oh, S., Kim, H.M., Jho, S., Kim, S. et al. (2013) The tiger genome and comparative analysis with lion and snow leopard genomes. Nat. Commun., 4, 2433.
13. Hulsen, T., de Vlieg, J. and Alkema, W. (2008) BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics, 9, 488.
14. Pirooznia, M., Nagarajan, V. and Deng, Y. (2007) GeneVenn - a web application for comparing gene lists using Venn diagrams. Bioinformation, 1, 420-422.
15. Kestler, H.A., Muller, A., Kraus, J.M., Buchholz, M., Gress, T.M., Liu, H., Kane, D.W., Zeeberg, B.R. and Weinstein, J.N. (2008) Venn Master: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics, 9, 67.
16. Wang, Y., Thilmony, R. and Gu, Y.Q. (2014) Net Venn: an integrated network analysis web platform for gene lists. Nucleic Acids Res., 42, W161-W166.
17. Blom, J., Albaum, S.P., Doppmeier, D., Puhler, A., Vorholter, F.J., Zakrzewski, M. and Goesmann, A. (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, 10, 154.
18. Curtis, D.S., Phillips, A.R., Callister, S.J., Conlan, S. and McCue, L.A. (2013) SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes. Bioinformatics, 29, 2641-2642.
19. Cunningham, F., Amode, M.R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
20. Li, L., Stoeckert, C.J. Jr and Roos, D.S. (2003) Ortho MCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
21. Remm, M., Storm, C.E. and Sonnhammer, E.L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314, 1041-1052.
22. Enright, A.J., Van Dongen, S. and Ouzounis, C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
23. Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
24. Moreno-Hagelsieb, G. and Hudy-Yuffa, B. (2014) Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT. BMC Res. Notes, 7, 651.
25. Ward, N. and Moreno-Hagelsieb, G. (2014) Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PLoS One, 9, e101850.
26. Ekseth, O.K., Kuiper, M. and Mironov, V. (2014) orthAgogue: an agile tool for the rapid prediction of orthology relations. Bioinformatics, 30, 734-736.
27. Uni Prot, C. (2015) UniProt: a hub for protein information. Nucleic Acids Res., 43, D204-D212.
28. McCarthy, F.M., Wang, N., Magee, G.B., Nanduri, B., Lawrence, M.L., Camon, E.B., Barrell, D.G., Hill, D.P., Dolan, M.E., Williams, W.P. et al. (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics, 7, 229.
29. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
30. Bailey, T.L., Boden, M., Buske, F.A., Frith, M., Grant, C.E., Clementi, L., Ren, J., Li, W.W. and Noble, W.S. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
31. Price, M.N., Dehal, P.S. and Arkin, A.P. (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
32. Bardou, P., Mariette, J., Escudie, F., Djemiel, C. and Klopp, C. (2014) jvenn: an interactive Venn diagram viewer. BMC Bioinformatics, 15, 293.
33. Jia, J., Zhao, S., Kong, X., Li, Y., Zhao, G., He, W., Appels, R., Pfeifer, M., Tao, Y., Zhang, X. et al. (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 496, 91-95.
34. Creevey, C.J., Muller, J., Doerks, T., Thompson, J.D., Arendt, D. and Bork, P. (2011) Identifying single copy orthologs in Metazoa. PLoS Comput. Biol., 7, e1002269.
35. Lopes, C.T., Franz, M., Kazi, F., Donaldson, S.L., Morris, Q. and Bader, G.D. (2010) CytoscapeWeb: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.