Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Altenhoff, Adrian M ^a,b   Gil, Manuel ^a,b   Gonnet, Gaston H ^a,b   Dessimoz, Christophe ^a,b,c  

^a ETH ZURICH   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA BASE; GENE; GENE FUNCTION; GENETIC ALGORITHM; GENOME; HEREDITY; HIERARCHICAL ORTHOLOGOUS GROUP; HUMAN; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOGY; PHYLOGENETIC TREE; SIMULATION; TAXONOMIC RANK;

ALGORITHMS; DATABASES, GENETIC; GENOMICS; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84872287798     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0053786     Document Type: Article

References (35)

1. Fitch WM, (1970) Distinguishing homologous from analogous proteins. Syst Zool 19: 99-113.
2. Kristensen DM, Wolf YI, Mushegian AR, Koonin EV, (2011) Computational methods for Gene Orthology inference. Briefings in bioinformatics 12: 379-391.
3. Altenhoff AM, Dessimoz C (2012) Inferring orthology and paralogy. In: Anisimova M, editor, Evolutionary Genomics, Clifton, NJ, USA: Methods in Molecular Biology. 259-279.
4. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N, (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 96: 2896-2901.
5. Wall DP, Fraser HB, Hirsh AE, (2003) Detecting putative orthologs. Bioinformatics 19: 1710-1711.
6. Remm M, Storm C, Sonnhammer E, (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-52.
7. Roth AC, Gonnet GH, Dessimoz C, (2008) The algorithm of OMA for large-scale orthology inference. BMC Bioinformatics 9: 518.
8. Altenhoff AM, Dessimoz C, (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 5: e1000262.
9. Boeckmann B, Robinson-Rechavi M, Xenarios I, Dessimoz C, (2011) Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Brief Bioinform 12: 474-484.
10. Li L, Stoeckert CJJ, Roos DS, (2003) Orthomcl: identi_cation of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
11. Chen C, Natale DA, Finn RD, Huang H, Zhang J, et al. (2011) Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS ONE 6: e18910.
12. Miele V, Penel S, Duret L, (2011) Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics 12: 116.
13. Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, et al. (2012) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research 40: D284-9.
14. Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EV, (2011) OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Research 39: D283-8.
15. Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C, (2011) OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 39: D289-D294.
16. van der Heijden RT, Snel B, van Noort V, Huynen MA, (2007) Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics 8: 83.
17. Vilella AJJ, Severin J, Ureta-Vidal A, Durbin R, Heng L, et al. (2009) Ensemblcompara genetrees: Analysis of complete, duplication aware phylogenetic trees in vertebrates. Genome research 19: 327-335.
18. Wapinski I, Pfeffer A, Friedman N, Regev A, (2007) Natural history and evolutionary principles of gene duplication in fungi. Nature 449: 54-61.
19. Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T, (2008) Phylomedb: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res 36: D491-D496.
20. Chen F, Mackey AJ, Stoeckert CJ, Roos DS, (2006) Orthomcl-db: querying a comprehensive multispecies collection of ortholog groups. Nucleic Acids Res 34: D363-D368.
21. Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, et al. (2010) Inparanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res 38: D196-D203.
22. DeLuca TF, Wu IH, Pu J, Monaghan T, Peshkin L, et al. (2006) Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics 22: 2044-2046.
23. Jothi R, Zotenko E, Tasneem A, Przytycka TM, (2006) Coco-cl: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics 22: 779-788.
24. Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C, (2012) ALF-A Simulation Framework for Genome Evolution. Molecular Biology and Evolution 29: 1115-1123.
25. Yang Z, Nielsen R, Goldman N, Pedersen AMK, (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 432-449.
26. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2009) Database resources of the national center for biotechnology information. Nucleic acids research 37: D5-15.
27. Linard B, Thompson J, Poch O, Lecompte O, (2011) Orthoinspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics 12: 11.
28. Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, et al. (2011) Orthology prediction methods: a quality assessment using curated protein families. BioEssays 33: 769-780.
29. Dessimoz C, Boeckmann B, Roth A, Gonnet GH, (2006) Detecting non-orthology in the cog database and other approaches grouping orthologs using genome-specific best hits. Nucleic Acids Res 34: 3309-3316.
30. Gonnet GH, Hallett MT, Korostensky C, Bernardin L, (2000) Darwin v. 2.0: An interpreted computer language for the biosciences. Bioinformatics 16: 101-103.
31. Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, et al. (2010) A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 26: 1481-1487.
32. Neyman J (1971) Molecular studies of evolution: a source of novel statistical problems. In: Gupta S, Yackel J, editors, Statistical decision theory and related topics, Academic Press, New York. 1-27.
33. Tarjan RE, van Leeuwen J, (1984) Worst-case analysis of set union algorithms. Journal of the ACM 31: 245-281.
34. Ford L, Fulkerson D, (1956) Maximal ow through a network. Canadian Journal of Mathematics 8: 399-404.
35. Karger DR, Stein C, (1996) A new approach to the minimum cut problem. J ACM 43: 601-640.