Some algorithmic challenges in genome-wide ortholog assignment

Journal of Computer Science and Technology

Volumn 25, Issue 1, 2010, Pages 42-52

  Jiang, Tao ^a,b  

^a University of California Riverside   (United States)

^b TSINGHUA UNIVERSITY   (China)

Author keywords

Algorithm; Comparative genomics; Computational biology; Genome rearrangement; Ortholog assignment

Indexed keywords

ALGORITHMS; BIOINFORMATICS; BIOLOGY;

ALGORITHMIC PROBLEMS; COMPARATIVE GENOMICS; COMPUTATIONAL BIOLOGY; FUNCTIONAL GENOMICS; GENOME REARRANGEMENTS; ORTHOLOGS; PHYLOGENETIC ANALYSIS; TRANSPOSITION DISTANCES;

GENES;

EID: 75749121403     PISSN: 10009000     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11390-010-9304-6     Document Type: Article

References (53)

1. WM Fitch 1970 Distinguishing homologous from analogous proteins Syst. Zool. 19 2 99 113 10.2307/2412448 814892
2. EV Koonin 2005 Orthologs, paralogs, and evolutionary genomics Annu. Rev. Genet. 39 309 338 10.1146/annurev.genet.39.073003.114725 (Pubitemid 43011118)
3. M Remm C Storm E Sonnhammer 2001 Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J. Mol. Biol. 314 5 1041 1052 10.1006/jmbi.2000.5197 (Pubitemid 34073068)
4. D Sankoff 1999 Genome rearrangement with gene families Bioinformatics 15 11 909 917 10.1093/bioinformatics/15.11.909
5. RL Tatusov MY Galperin DA Natale EV Koonin 2000 The COG database: A tool for genome-scale analysis of protein functions and evolution Nucleic Acids Res. 28 1 33 36 10.1093/nar/28.1.33
6. RL Tatusov EV Koonin DJ Lipman 1997 A genomic perspective on protein families Science 278 631 637 10.1126/science.278.5338.631 (Pubitemid 27464953)
7. S Altschul T Madden A Schaffer J Zhang Z Zhang W Miller D Lipman 1997 Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Research 25 17 3389 3402 10.1093/nar/25.17.3389 (Pubitemid 27359211)
8. Chen X, Zheng J, Fu Z, Nan P, Zhong Y, Lonardi S, Jiang T. Computing the assignment of orthologous genes via genome rearrangement. In Proc. the 3rd Asia Pacific Bioinformatics Conf. (APBC 2005), Singapore, Jan. 17-21, 2005, pp.363-378.
9. X Chen J Zheng Z Fu P Nan Y Zhong S Lonardi T Jiang 2005 The assignment of orthologous genes via genome rearrangement IEEE/ACM Transactions on Computational Biology and Bioinformatics 2 4 302 315 10.1109/TCBB.2005.48 (Pubitemid 43060406)
10. Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T. A parsimony approach to genome-wide ortholog assignment. In Proc. the 10th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Venice, Italy, April 2-5, 2006, pp.578-594.
11. Z Fu X Chen V Vacic P Nan Y Zhong T Jiang 2007 MSOAR: A high-throughput ortholog assignment system based on genome rearrangement Journal of Computational Biology 14 9 1160 1175 10.1089/cmb.2007.0048 2358327 (Pubitemid 350100393)
12. Y Lee R Sultana G Pertea J Cho S Karamycheva J Tsai B Parvizi F Cheung V Antonescu J White I Holt F Liang J Quackenbush 2002 Cross-referencing eukaryotic genomes: TIGR orthologous gene alignments (TOGA) Genome Res. 12 3 493 502 10.1101/gr.212002 (Pubitemid 34233026)
13. L Li C Stoeckert D Roos 2003 OrthoMCL: Identification of ortholog groups for eukaryotic genomes Genome Res. 13 9 2178 2189 10.1101/gr.1224503 (Pubitemid 37161775)
14. YP Yuan O Eulenstein M Vingron P Bork 1998 Towards detection of orthologues in sequence databases Bioinformatics 14 3 285 289 10.1093/bioinformatics/14.3.285
15. C Storm E Sonnhammer 2002 Automated ortholog inference from phylogenetic trees and calculation of orthology reliability Bioinformatics 18 1 92 99 10.1093/bioinformatics/18.1.92
16. SB Cannon ND Young 2003 OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies BMC Bioinformatics 4 1 35 10.1186/1471-2105-4-35 (Pubitemid 38751235)
17. XH Zheng F Lu Z Wang F Zhong J Hoover R Mural 2005 Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs Bioinformatics 21 6 703 710 10.1093/bioinformatics/bti045 (Pubitemid 40439406)
18. A Kuzniar R van Ham S Pongor J Leunissen 2008 The quest for orthologs: Finding the corresponding gene across genomes Trends in Genetics 24 11 539 550 10.1016/j.tig.2008.08.009
19. N El-Mabrouk 2002 Reconstructing an ancestral genome using minimum segments duplications and reversals Journal of Computer and System Sciences 65 3 442 464 1058.68529 10.1016/S0022-0000(02)00003-X 1955942
20. M Marron K Swenson B Moret 2004 Genomic distances under deletions and insertions Theoretical Computer Science 325 3 347 360 1071.92503 10.1016/j.tcs.2004.02.039 2090048
21. Swenson K, Marron M, Earnest-DeYoung J. Moret B. Approximating the true evolutionary distance between two genomes. In Proc. the 7th SIA Workshop on Algorithm Engineering & Experiments, Vancouver, Canada, Jan. 22, 2005, pp.121-125.
22. Swenson K, Pattengale N, Moret B. A framework for orthology assignment from gene rearrangement data. In Proc. the 3rd RECOMB Workshop on Comparative Genomics (RECOMB-CG2005), Dublin, Ireland, Sept. 18-20, 2005, LNCS 3678, Springer, pp.153-166.
23. Hannenhalli S, Pevzner P. Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals. J. ACM, 1999, 46(1): 1-27;
24. extended abstract in Proc. ACM STOC, Las Vegas, USA, May 23-June 1, 1995, pp.178-189.
25. Shi G, Zhang L, Jiang T. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. In Proc. the 8th LSS Computational Systems Bioinformatics Conference, Stanford, USA, August 10-12, 2009, pp.12-24.
26. A Bairoch R Apweiler CH Wu WC Barker B Boeckmann S Ferro E Gasteiger H Huang R Lopez M Magrane MJ Martin DA Natale C O'Donovan N Redaschi LS Yeh 2005 The Universal Protein Resource (UniProt) Nucleic Acids Res. 33 Database Issue D154 D159 10.1093/nar/gki070 (Pubitemid 40207850)
27. http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/hcop.pl.
28. ftp://ftp.pantherdb.org/sequence classifications/.
29. http://www.jax.org.
30. M Ozery-Flato R Shamir 2003 Two notes on genome rearragnements Journal of Bioinformatics and Computational Biology 1 1 71 94 10.1142/S0219720003000198
31. G Tesler 2002 Efficient algorithms for multichromosomal genome rearrangements Journal of Computer and System Sciences 65 3 587 609 1059.68160 10.1016/S0022-0000(02)00011-9 1955950
32. Hannenhalli S, Pevzner P A. Transforming men into mice (polynomial algorithm for genomic distance problem). In Proc. IEEE 36th Ann. Symp. Foundations of Comp. Sci. Milwaukee, USA, Oct. 23-25, 1995, pp.581-592.
33. D Christie R Irving 2001 Sorting strings by reversals and by transpositions SIAM J. Discrete Math. 14 2 193 206 0968.68116 10.1137/S0895480197331995 1856006 (Pubitemid 33701228)
34. Kaplan H, Shamir R, Tarjan R. Faster and simpler algorithm for sorting signed permutations by reversals. In Proc. the 8th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, USA, Jan. 5-7, 1997, pp.344-351.
35. D Bader B Moret M Yan 2001 A linear-time algorithm for computing inversion distance between signed permutations with an experimental study Journal of Computational Biology 8 5 483 491 10.1089/106652701753216503 (Pubitemid 33044073)
36. A Radcliffe A Scott E Wilmer 2005 Reversals and transpositions over finite alphabets SIAM J. Discrete Math. 19 1 224 244 1086.68094 10.1137/S0895480103433550 2178356 (Pubitemid 43310276)
37. Caprara A. Sorting by reversals is difficult. In Proc. the First Annual International Conference on Computational Molecular Biology, Santa Fe, USA, Jan. 20-23, 1997, pp.75-83.
38. A Caprara 1999 Sorting permutations by reversals and Eulerian cycle decompositions SIAM J. Discrete Math. 12 1 91 110 0916.68074 10.1137/S089548019731994X 1666069
39. V Bafna PP Genome 1996 Genome rearrangements and sorting by reversals SIAM J. Comput. 25 2 272 289 0844.68123 10.1137/S0097539793250627 1379301 extended abstract appeared in Proc. IEEE FOCS 1993, Palo Alto, USA, Nov. 3-5, 1993, pp.148-157
40. J Kececioglu D Sankoff 1995 Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement Algorithmica 13 1/2 180 210 0831.92014 10.1007/BF01188586 1304314
41. G Lin T Jiang 2004 A further improved approximation algorithm for breakpoint graph decomposition Journal of Combinatorial Optimization 8 2 183 194 1088.68182 10.1023/B:JOCO.0000031419.12290.2b 2071377
42. Q Gu S Peng H Sudborough 1999 A 2-approximation algorithm for genome rearrangements by reversals and transpositions Theoret. Comput. Sci. 210 2 327 339 0915.68033 10.1016/S0304-3975(98)00092-9 1655456
43. T Hartman R Sharon 2005 A 1.5-approximation algorithm for sorting by transpositions and transreversals Journal of Computer and System Sciences 70 3 300 320 10.1016/j.jcss.2004.12.006 2129864 (Pubitemid 40391412)
44. V Bafna P Pevzner 1998 Sorting by transpositions SIAM J. Discrete Math. 11 2 224 240 0973.92014 10.1137/S089548019528280X 1617154
45. Goldstein A, Kolman P, Zheng J. Minimum common string partition problem: Hardness and approximations. In Proc. the 15th International Symposium on Algorithms and Computation, Hong Kong, China, Dec. 20-22, 2004, pp.484-495. (Pubitemid 39745101)
46. Chrobak M, Kolman P, Sgall J. The greedy algorithm for the minimum common string partition problem. In Proc. the 7th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, Cambridge, USA, Aug. 22-24, 2004, LNCS 3122, Springer, pp.84-95.
47. Kolman P. Approximating aeversal distance for strings with bounded number of duplicates. In Proc. the 30th International Symposium on Mathematical Foundations of Computer Science, Gdansk, Poland, Aug. 29-Sept. 2, 2005, pp.580-590.
48. Halldorsson M M. Approximating discrete collections via local improvements. In Proc. the Sixth Annual ACM-SIAM Symp. Discrete Algorithms, San Francisco, USA, Jan. 22-24, 1995, pp.160-169.
49. Kolman P, Walen T. Reversal distance for strings with duplicates: Linear time approximation using hitting set. In Proc. the 4th Workshop on Approximation and Online Algorithms, Zurich, Switzerland, Sept. 14-15, 2006, pp.279-289.
50. G Bourque P Pevzner 2002 Genome-scale evolution: Reconstructing gene orders in the ancestral species Genome Research 12 1 26 36
51. D Sankoff M Blanchette 1998 Multiple genome rearrangement and breakpoint phylogeny Journal of Computational Biology 5 3 555 570 10.1089/cmb.1998.5.555
52. Z Fu T Jiang 2008 Clustering of main orthologs for multiple genomes Journal of Bioinformatics and Computational Biology 6 3 573 584 10.1142/S0219720008003540 2441477 (Pubitemid 351895194)
53. L Wang T Jiang E Lawler 1996 Approximation algorithms for tree alignment with a given phylogeny Algorithmica 16 3 302 315 10.1007/BF01955679 1400054 (Pubitemid 126418830)