Computing the assignment of orthologous genes via genome rearrangement

Series on Advances in Bioinformatics and Computational Biology

Volumn 1, Issue , 2005, Pages 363-378

  Chen, X ^a   Zheng, J ^a   Fu, Z ^a   Nan, P ^b   Zhong, Y ^b   Lonardi, S ^a   Jiang, T ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DNA SEQUENCES; EVOLUTIONARY ALGORITHMS; HEURISTIC ALGORITHMS;

COMPARATIVE GENOMICS; CYCLE DECOMPOSITIONS; EVOLUTIONARY EVENTS; EVOLUTIONARY RELATIONSHIPS; GENOME REARRANGEMENTS; GENOME SEQUENCE DATA; HIGH THROUGHPUT SYSTEMS; OPTIMIZATION PROBLEMS;

GENES;

EID: 84863067228     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1142/9781860947322_0037     Document Type: Conference Paper

References (21)

1. W.M. Fitch. Distinguishing homologous from analogous proteins. Syst. Zool. 19, pp.99-113, 1970.
2. E. Sonnhammer and E. Koonin. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 16, pp.227-231, 2000.
3. D. Sankoff. Genome rearrangement with gene families. Bioinformatics, 15(11): 909-917, 1999. (Pubitemid 30103161)
4. R.L. Tatusov, E.V. Koonin and D.J. Lipman. A genomic perspective on protein families. Science 278: 631-637.
5. R.L. Tatusov, M.Y. Galperin, D.A. Natale and E.V. Koonin. The COG database: A tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36, 2000. (Pubitemid 30047708)
6. M. Remm, C. Storm and E. Sonnhammer. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol., 314, pp.1041-1052, 2001. (Pubitemid 34073068)
7. S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17): 3389-3402, 1997. (Pubitemid 27359211)
8. S. Hannenhalli and P. Pevzner. Transforming cabbage into turnip (Polynomial algorithm for sorting signed permutations by reversals). Proc. 27th Annual ACM Symposium on the Theory of Computing. pp.178-187, 1995.
9. Y.P. Yuan, O. Eulenstein, M. Vingron and P. Bork. Towards detection of orthologues in sequence databases. Bioinformatics, 14(3), pp.285-289, 1998. (Pubitemid 28395865)
10. C. Storm and E. Sonnhammer. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics, 18(1), 2002.
11. S.B. Cannon and N.D. Young. OrtholParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. BMC Bioinformatics, 4(1):35, 2003.
12. H. Kaplan, R. Shamir and R. Tarjan. Faster and simpler algorithm for sorting signed permutations by reversals. In Proceedings of the 8th Annual ACM-SIAM Symposium on Discrete Algo rithms, pp. 344-351, 1997.
13. D. Bader, B. Moret and M. Yan. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. Journal of Computational Biology, 8(5):483-491, 2001. (Pubitemid 33044073)
14. N. El-Mabrouk. Reconstructing an ancestral genome using minimum segments duplications and reversals. Journal of Computer and System Sciences, 65, pp.442-464, 2002. (Pubitemid 41161949)
15. J. Tang and B. Moret. Phylogenetic reconstruction from gene rearrangement data with unequal gene contents. Proc. 8th Workshop on Algorithms and Data Structures (WADS'03), 37-46, 2003.
16. K. Chao and W. Miller. Linear space algorithms that build local alignments from fragments. Algorithmica, 13: 106-134, 1995.
17. D. Christie and R. Irving. Sorting strings by reversals and by transpositions. SIAM J. Discrete Math. Vol. 14(2). pp.193-206, 2001. (Pubitemid 33701228)
18. A. Goldstein, P. Kolman and J. Zheng. Minimum common string partition problem: hardness and approximations. Accepted by ISAAC'04, 2004.
19. A. Caprara. Sorting permutations by reversals and Eulerian cycle decompositions. SIAM J. Discrete Math. Vol. 12(1), pp.91-110, 1999.
20. P. Pevzner and G. Tesler. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Research, 13: 37-45, 2003.
21. H.M. Wain, et al.. Guidelines for human gene nomenclature. Genomics, 79(4), pp.464-470, 2002. (Pubitemid 34274283)