Clustering of main orthologs for multiple genomes

Journal of Bioinformatics and Computational Biology

Volumn 6, Issue 3, 2008, Pages 573-584

  Fu, Zheng ^a   Jiang, Tao ^a  

^a University of California Riverside ^*  (United States)

Author keywords

Comparative genomics; Genome rearrangement; Ortholog

Indexed keywords

ACCURACY; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; CONFERENCE PAPER; GENE CLUSTER; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE REARRANGEMENT; GENE SEQUENCE; GENOME ANALYSIS; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; NONHUMAN; ORTHOLOGY; PREDICTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VALIDATION PROCESS;

ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; BASE SEQUENCE; CHROMOSOME MAPPING; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HUMANS; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

RATTUS;

EID: 46049121338     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720008003540     Document Type: Conference Paper

References (26)

1. Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T, A parsimony approach to genomewide ortholog assignment, in Proc 10th Annual International RECOMB Conference, pp. 578-594, 2006.
2. Fitch WM, Distinguishing homologous from analogous proteins, Syst Zool 19:99-113, 1970.
3. Tatusov RL, Koonin E, Lipman DJ, A genomic perspective on protein families, Science 278:631-637, 1997.
4. Tatusov RL, Galperin MY, Natale DA, Koonin EV, The COG database: A tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Res 28:33-36, 2000.
5. Tatusov RL, Natale DA, Jackson JD et al., The COG database: An update version includes eukaryotes, BMC Bioinformatics 4 41-54, 2003.
6. Lee Y, Sultana R, Pertea G et al., Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA), Genome Res 12 493-502, 2002.
7. Remm M, Storm CE, Sonnhammer EL, Automatic clustering of orthologs and inparalogs from pairwise species comparisons, J Mol Biol 314 1041-1052, 2001.
8. Alexeyenko A, Tamas I, Liu I, Sonnhammer ELL, Automatic clustering of orthologs and inpaxalogs shared by multiple proteomes, Bioinformatics 22:9-15, 2006.
9. Li L, Stoeckert C, Roos D, OrthoMCL: Identification of ortholog groups for eukaryotic genomes, Genome Res 13:2178-2189, 2003.
10. Dufayard J, Duret L, Penel S, Gouy M, Rechenmann F, Perriere G, Tree pattern matching in phylogenetic trees: Automatic search for orthologs or paralogs in homologous gene sequence database, Bioinformatics 21:2596-2603, 2005.
11. Li H, Coghlan A, Ruan J et al., TreeFam: A curated database of phylogenetic trees of animal gene families, Nucleic Acids Res 34:D572-D580, 2006.
12. Goodstadt L, Ponting C, Phylogenetic reconstruction of orthology, paralogy and conserved synteny for dog and human, PLoS Biol 1 e45, 2003.
13. Storm CE, Sonnhammer EL, Automated ortholog inference from phylogenetic trees and calculation of orthology reliability, Bioinformatics 18:92-99, 2002.
14. Zmasek CM, Eddy SR, RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics 3 14, 2002.
15. Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R, OrthologID: Automation of genome-scale ortholog identification within a parsimony framework, Bioinformatics 22:699-707, 2006.
16. Dehal P, Boore J, Two rounds of whole genome duplication in the ancestral vertebrate, PLoS Biol 3:1700-1708, 2005.
17. Eisen JA, Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis, Genome Res 8 163-167, 1998.
18. Sankoff D, Genome rearrangement with gene families, Bioinformatics 15:909-917, 1999.
19. Eyre TA, Wright MW, Lush MJ, Bruford EA, HCOP: A searchable database of human orthology predictions, Brief Bioinform 8:2-5, 2007.
20. Eppig JT, Bult CJ, Kadin JA et al., The Mouse Genome Database (MGD): From genes to mice: A community resource for mouse biology, Nucleic Acids Res 33:D471-D475, 2005.
21. Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania, A, PANTHER: A library of protein families and sub-families indexed by function, Genome Res 13 2129-2141, 2003.
22. Kann V, Maximum bounded 3-dimensional matching is MAX SNP-complete, Inf Process Lett 37:27-35, 1991.
23. Bandelt H, Crama Y, Spieksma F, Approximation algorithms for multi-dimensional assignment problems with decomposable costs, Discrete Appl Math 49:25-50, 1994.
24. Papadimitriou CH, Steiglitz K, Combinatorial Optimization: Algorithms and Complexity, Dover, Mineola, NY, 1998.
25. Karolchik D, Baertsch R, Diekhans M et al., The UCSC Genome Browser Database, Nucleic Acids Res 31:51-54, 2003.
26. Bairoch A, Apweiler R, Wu CH et al., The Universal Protein Resource (UniProt), Nucleic Acids Res 33:D154-D159, 2005.