Assignment of orthologous genes via genome rearrangement

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 2, Issue 4, 2005, Pages 302-314

  Chen, Xin ^a   Zheng, Jie ^a   Fu, Zheng ^a,c   Nan, Peng ^b,d   Zhong, Yang ^b,d,e   Lonardi, Stefano ^a,c,f   Jiang, Tao ^{a,b,c,e,f,g,h}  

^a University of California Riverside   (United States)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d FUDAN UNIVERSITY   (China)

^e PEKING UNIVERSITY   (China)

^f IEEE   (United States)

^g Center for Plant Cell Biology   (United States)

^h TSINGHUA UNIVERSITY   (China)

Author keywords

Comparative genomics; Gene duplication; Genome rearrangement; Ortholog; Paralog; Reversal

Indexed keywords

COMPARATIVE GENOMICS; GENE DUPLICATION; GENOME REARRANGEMENT; ORTHOLOG; PARALOG; REVERSAL;

ALGORITHMS; BIOTECHNOLOGY; DATA REDUCTION; GENETIC ENGINEERING; HEURISTIC METHODS; ITERATIVE METHODS; OPTIMIZATION;

GENES;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGY; COMPARATIVE STUDY; COMPUTER PROGRAM; DNA SEQUENCE; GENE REARRANGEMENT; GENETIC DATABASE; GENETICS; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; MOUSE; RAT; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; X CHROMOSOME;

ALGORITHMS; ANIMALS; CHROMOSOMES, HUMAN, X; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; GENOME; GENOMICS; HUMANS; MICE; RATS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; X CHROMOSOME;

EID: 30344450783     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2005.48     Document Type: Article

References (28)

1. 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, vol. 25, no. 17, pp. 3389-3402, 1997.
2. D. Bader, B. Moret, and M. Yan, "A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study," J. Computational Biology, vol. 8, no. 5, pp. 483-491, 2001.
3. G. Bourque and P. Pevzner, "Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species," Genome Research, vol. 12, pp. 26-36, 2002.
4. S.B. Cannon and N.D. Young, "OrtholParaMap: Distinguishing Orthologs from Paralogs by Integrating Comparative Genome Data and Gene Phylogenies," BMC Bioinformatics, vol. 4, no. 1, p. 35, 2003.
5. A. Caprara, "Sorting by Reversals Is Difficult," Proc. First Ann. Int'l Conf. Computational Molecular Biology, pp. 75-83, 1997.
6. A. Caprara, "Sorting Permutations by Reversals and Eulerian Cycle Decompositions," SIAM J. Discrete Math., vol. 12, no. 1, pp. 91-110, 1999.
7. D. Christie and R. Irving, "Sorting Strings by Reversals and by Transpositions," SIAM J. Discrete Math., vol. 14, no. 2, pp. 193-206, 2001.
8. K. Chao and W. Miller, "Linear Space Algorithms that Build Local Alignments from Fragments," Algorithmica, vol. 13, pp. 106-134, 1995.
9. N. El-Mabrouk, "Reconstructing an Ancestral Genome Using Minimum Segments Duplications and Reversals," J. Computer and System Sciences, vol. 65, pp. 442-464, 2002.
10. W.M. Fitch, "Distinguishing Homologous from Analogous Proteins," Systematic Zoology, vol. 19, pp. 99-113, 1970.
11. Z. Fu, "Assignment of Orthologous Genes for Multichromosomal Genomes Using Genome Rearrangement," UCR CS technical report, 2004.
12. A. Goldstein, P. Kolman, and J. Zheng, "Minimum Common String Partition Problem: Hardness and Approximations," Proc. 15th Int'l Symp. Algorithms and Computation (ISAAC), pp. 473-484, 2004.
13. M.M. Halldorsson, "Approximating Discrete Collections via Local Improvements," Proc. Sixth ACM-SIAM Symp. Discrete Algorithms, pp. 160-169, 1995.
14. S. Hannenhalli and P. Pevzner, "Transforming Cabbage into Turnip (Polynomial Algorithm for Sorting Signed Permutations by Reversals)," Proc. 27th Ann. ACM Symp. Theory of Computing, pp. 178-187, 1995.
15. H. Kaplan, R. Shamir, and R. Tarjan, "Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals," Proc. Eighth Ann. ACM-SIAM Symp. Discrete Algorithms, pp. 344-351, 1997.
16. P. Pevzner and G. Tesler, "Genome Rearrangements in Mammalian Evolution: Lessons from Human and Mouse Genomes," Genome Research, vol. 13, pp. 37-45, 2003.
17. M. Remm, C. Storm, and E. Sonnhammer, "Automatic Clustering of Orthologs and In-Paralogs from Pairwise Species Comparisons," J. Molecular Biology, vol. 314, pp. 1041-1052, 2001.
18. D. Sankoff, "Genome Rearrangement with Gene Families," Bioinformatics, vol. 15, no. 11, pp. 909-917, 1999.
19. E. Sonnhammer and E. Koonin, "Orthology, Paralogy and Proposed Classification for Paralog Subtypes," Trends in Genetics, vol. 16, pp. 227-231, 2000.
20. P. Slonimski, M. Mosse, P. Golik, A. Henault, Y. Diaz, J. Risler, J. Comet, J. Aude, A. Wozniak, E. Glemet, and J. Codani, "The First Laws of Genomics," Microbial & Comparative Genomics, vol. 3, p. 46, 1998.
21. K. Swenson, M. Marron, J. Earnest-DeYoung, and B. Moret, "Approximating the True Evolutionary Distance between Two Genomes," Technical Report TR-CS-2004-15, Univ. of New Mexico, 2004.
22. C. Storm and E. Sonnhammer, "Automated Ortholog Inference from Phylogenetic Trees and Calculation of Orthology Reliability," Bioinformatics, vol. 18, no. 1, 2002.
23. 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 Research, vol. 28, pp. 33-36, 2000.
24. R.L. Tatusov, E.V. Koonin, and D.J. Lipman, "A Genomic Perspective on Protein Families," Science, vol. 278, pp. 631-637, 1997.
25. J. Tang and B. Moret, "Phylogenetic Reconstruction from Gene Rearrangement Data with Unequal Gene Contents," Proc. Eighth Workshop Algorithms and Data Structures, (WADS '03) pp. 37-46, 2003.
26. H.M. Wain, E.A. Bruford, R.C. Lovering, M.J. Lush, M.W. Wright, and S. Povey, "Guidelines for Human Gene Nomenclature," Genomics, vol. 79, no. 4, pp. 464-470, 2002.
27. L. Wang and T. Warnow, "Estimating True Evolutionary Distances between Genomes," Proc. 33rd Ann. ACM Symp. Theory of Computing, pp. 637-646, 2001.
28. Y.P. Yuan, O. Eulenstein, M. Vingron, and P. Bork, "Towards Detection of Orthologues in Sequence Databases," Bioinformatics, vol. 14, no. 3, pp. 285-289, 1998.