SCJ: A breakpoint-like distance that simplifies several rearrangement problems

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 8, Issue 5, 2011, Pages 1318-1329

  Feijão, Pedro ^a   Meidanis, João ^a,b  

^a UNIVERSITY OF CAMPINAS   (Brazil)

^b SCYLLA BIOINFORMATICS   (Brazil)

Author keywords

Biology and genetics; combinatorial algorithms; computations on discrete structures

Indexed keywords

BIOLOGY AND GENETICS; BREAKPOINT DISTANCE; COMBINATORIAL ALGORITHM; COMPUTATIONS ON DISCRETE STRUCTURES; DISTANCE MEASURE; GENOME COMPARISON; GENOME REARRANGEMENTS; MEDIAN PROBLEM; MULTICHROMOSOMAL GENOMES; NP-HARD; POLYNOMIAL-TIME ALGORITHMS;

ALGORITHMS; COMPUTATIONAL COMPLEXITY; POLYNOMIAL APPROXIMATION;

GENES;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; GENE REARRANGEMENT; GENETICS; GENOMICS; METHODOLOGY; PHYLOGENY;

ALGORITHMS; GENE REARRANGEMENT; GENOMICS; MODELS, GENETIC; PHYLOGENY;

EID: 79960901597     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.34     Document Type: Article

References (50)

1. A.H. Sturtevant and T. Dobzhansky, "Inversions in the Third Chromosome of Wild Races of Drosophila Pseudoobscura, and Their Use in the Study of the History of the Species," Proc. Nat'l Academy of Sciences USA, vol. 22, no. 7, pp. 448-450, 1936.
2. B. McClintock, "The Origin and Behavior of Mutable Loci in Maize," Proc. Nat'l Academy of Sciences of USA, vol. 36, no. 6, pp. 344-355, 1950.
3. J.H. Nadeau and B.A. Taylor, "Lengths of Chromosomal Segments Conserved Since Divergence of Man and Mouse," Proc. Nat'l Academy of Sciences USA, vol. 81, no. 3, pp. 814-818, 1984. (Pubitemid 14199035)
4. S. Hannenhalli and P.A. Pevzner, "Transforming Cabbage into Turnip: (Polynomial Algorithm for Sorting Signed Permutations by Reversals)," Proc. 27th Ann. Symp. Theory of Computing (STOC '95), 1995.
5. S. Hannenhalli, "Polynomial-Time Algorithm for Computing Translocation Distance between Genomes," Discrete Applied Math., vol. 71, nos. 1-3, pp. 137-151, 1996. (Pubitemid 126391776)
6. D.A. Christie, "Sorting Permutations by Block-Interchanges," Information Processing Letters, vol. 60, pp. 165-169, 1996. (Pubitemid 126383390)
7. V. Bafna and P.A. Pevzner, "Sorting by Transpositions," SIAM J. Discrete Math., vol. 11, no. 2, pp. 224-240, 1998. (Pubitemid 128619806)
8. I. Elias and T. Hartman, "A 1.375-Approximation Algorithm for Sorting by Transpositions," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 369-379, Oct.-Dec. 2006. (Pubitemid 44950086)
9. S. Hannenhalli and P.A. Pevzner, "Transforming Men into Mice (Polynomial Algorithm for Genomic Distance Problem)," FOCS '95: Proc. 36th Ann. Symp. Foundations of Computer Science, pp. 581-592, 1995.
10. C. Mira and J. Meidanis, "Sorting by Block-Interchanges and Signed Reversals," Proc. Fourth Int'l Conf. Information Technology (ITNG '07), pp. 670-676, 2007.
11. Z. Dias and J. Meidanis, "Genome Rearrangements Distance by Fusion, Fission, and Transposition is Easy," Proc. Eighth Symp. String Processing and Information Retrieval (SPIRE '01), pp. 250-253, 2001.
12. C.L. Lu, Y.L. Huang, T.C. Wang, and H.-T. Chiu, "Analysis of Circular Genome Rearrangement by Fusions, Fissions and Block-Interchanges," BMC Bioinformatics, vol. 7, article no. 295, http://dx.doi.org/10.1186/1471- 2105-7-295, 2006.
13. S. Yancopoulos, O. Attie, and R. Friedberg, "Efficient Sorting of Genomic Permutations by Translocation, Inversion and Block Interchange," Bioinformatics, vol. 21, no. 16, pp. 3340-3346, http://dx.doi.org/10.1093/ bioinformatics/bti535, 2005. (Pubitemid 41222437)
14. S. Hannenhalli, C. Chappey, E.V. Koonin, and P.A. Pevzner, "Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case," Genomics, vol. 30, no. 2, pp. 299-311, 1995.
15. D. Sankoff, G. Sundaram, and J.D. Kececioglu, "Steiner Points in the Space of Genome Rearrangements," Int'l J. Foundations of Computer Science, vol. 7, no. 1, pp. 1-9, citeseer.ist.psu.edu/ sankoff96steiner.html, 1996.
16. E. Tannier, C. Zheng, and D. Sankoff, "Multichromosomal Median and Halving Problems under Different Genomic Distances," BMC Bioinformatics, vol. 10, no. 1, article no. 120, http://dx.doi.org/10.1186/1471-2105-10-120, Apr. 2009.
17. M. Blanchette, G. Bourque, and D. Sankoff, "Breakpoint Phylogenies," Proc. Genome Informatics Ser Workshop Genome Informatics, vol. 8, pp. 25-34, 1997.
18. D. Sankoff and M. Blanchette, "Multiple Genome Rearrangement and Breakpoint Phylogeny," J. Computational Biology, vol. 5, no. 3, pp. 555-570, 1998. (Pubitemid 28436301)
19. B.M. Moret, L.S. Wang, T. Warnow, and S.K. Wyman, "New Approaches for Reconstructing Phylogenies from Gene Order Data," Bioinformatics, vol. 17, Suppl 1, pp. S165-S173, 2001. (Pubitemid 33793507)
20. D.A. Bader, B.M. 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, http://dx.doi.org/10.1089/106652701753216503,2001.
21. B.M. Moret, A.C. Siepel, J. Tang, and T. Liu, "Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data," WABI: Proc. Second Int'l Workshop Algorithms in Bioinformatics, pp. 521-536, 2002.
22. D.H. Huson, S.M. Nettles, and T.J. Warnow, "Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction," J. Computational Biology, vol. 6, nos. 3/4, pp. 369-386, http://dx.doi.org/10.1089/ 106652799318337, 1999.
23. J. Tang and B.M.E. Moret, "Scaling Up Accurate Phylogenetic Reconstruction from Gene-Order Data," Bioinformatics, vol. 19, Suppl 1, pp. i305-i312, 2003.
24. G. Bourque and P.A. Pevzner, "Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species," Genome Research, vol. 12, no. 1, pp. 26-36, 2002. (Pubitemid 34065587)
25. M. Bernt, D. Merkle, and M. Middendorf, "Using Median Sets for Inferring Phylogenetic Trees," Bioinformatics, vol. 23, no. 2, pp. e129-e135, http://dx.doi.org/10.1093/bioinformatics/btl300,Jan. 2007. (Pubitemid 46189647)
26. Z. Adam and D. Sankoff, "The ABCs of MGR with DCJ," Evolutionary Bioinformatics Online, vol. 4, pp. 69-74, 2008. (Pubitemid 351552417)
27. M. Bader, M.I. Abouelhoda, and E. Ohlebusch, "A Fast Algorithm for the Multiple Genome Rearrangement Problem with Weighted Reversals and Transpositions," BMC Bioinformatics, vol. 9, p. 516, http://dx.doi.org/10. 1186/1471-2105-9-516, 2008.
28. J. Ma, L. Zhang, B.B. Suh, B.J. Raney, R.C. Burhans, W.J. Kent, M. Blanchette, D. Haussler, and W. Miller, "Reconstructing Contiguous Regions of an Ancestral Genome," Genome Research, vol. 16, no. 12, pp. 1557-1565, http://dx.doi.org/10.1101/gr.5383506, Dec.2006. (Pubitemid 44878494)
29. W.M. Fitch, "Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology," Systematic Zoology, vol. 20, pp. 406-416, 1971.
30. H. Zhao and G. Bourque, "Recovering True Rearrangement Events on Phylogenetic Trees," Comparative Genomics, G. Tesler and D. Durand, eds., Springer Berlin, pp. 149-161, http://dx.doi.org/10.1007/978-3-540-74960-8-12, 2007.
31. H. Zhao and G. Bourque, "Recovering Genome Rearrangements in the Mammalian Phylogeny," Genome Research, vol. 19, no. 5, pp. 934-942, http://dx.doi.org/10.1101/gr.086009.108, May 2009.
32. M.A. Alekseyev and P.A. Pevzner, "Breakpoint Graphs and Ancestral Genome Reconstructions," Genome Research, vol. 19, no. 5, pp. 943-957, http://dx.doi.org/10.1101/gr.082784.108, May 2009.
33. A. Caprara, "On the Tightness of the Alternating-Cycle Lower Bound for Sorting by Reversals," J. Combinatorial Optimization, vol. 3, pp. 149-182, http://dx.doi.org/10.1023/A:1009838309166,1999 (Pubitemid 129575312)
34. P. Medvedev and J. Stoye, "Rearrangement Models and Single-Cut Operations," RECOMB-CG '09: Proc. Int'l Workshop Comparative Genomics, pp. 84-97, 2009.
35. P. Pevzner and G. Tessler, "Transforming Men into Mice: The Nadeau-Taylor Chromosomal Breakage Model Revisited," RECOMB, pp. 247-256, ACM Press, 2003.
36. E. Tannier, C. Zheng, and D. Sankoff, "Multichromosomal Genome Median and Halving Problems," WABI '08: Proc. Eighth Int'l Workshop Algorithms in Bioinformatics, pp. 1-13, 2008.
37. A. Bergeron, J. Mixtacki, and J. Stoye, "A Unifying View of Genome Rearrangements," WABI '06: Proc. Sixth Int'l Workshop Algorithms in Bioinformatics, pp. 163-173, 2006. (Pubitemid 44609667)
38. R. Warren and D. Sankoff, "Genome Aliquoting with Double Cut and Join," BMC Bioinformatics, vol. 10, Suppl 1, p. S2, http://dx.doi.org/10. 1186/1471-2105-10-S1-S2, 2009.
39. I. Pe'er and R. Shamir, "The Median Problems for Breakpoints Are NP-Complete," Electronic Colloquium on Computational Complexity, vol. 71, no. 5, pp. 1-16, 1998.
40. D. Bryant, "The Complexity of the Breakpoint Median Problem," Technical Report CRM-2579, Centre de recherches mathematiques, Université de Montréal, 1998.
41. A. Caprara, "The Reversal Median Problem," INFORMS J. Computing, vol. 15, pp. 93-113, 2003. (Pubitemid 39042735)
42. L. Lovász and M.D. Plummer, "Matching Theory," Annals of Discrete Mathematics, vol. 29, North-Holland, 1986.
43. S. Ohno, Evolution by Gene Duplication. Springer-Verlag, 1970.
44. M. Kellis, B.W. Birren, and E.S. Lander, "Proof and Evolutionary Analysis of Ancient Genome Duplication in the Yeast Saccharomyces Cerevisiae," Nature, vol. 428, no. 6983, pp. 617-624, http://dx.doi.org/10. 1038/nature02424, 2004. (Pubitemid 38524797)
45. M.A. Alekseyev and P.A. Pevzner, "Colored de Bruijn Graphs and the Genome Halving Problem," IEEE/ACM Trans. Computational Biology Bioinformatics, vol. 4, no. 1, pp. 98-107, http://dx.doi.org/10.1109/TCBB.2007. 1002, Jan./Mar. 2007. (Pubitemid 46375819)
46. J. Mixtacki, "Genome Halving under DCJ Revisited," COCOON '08: Proc. 14th Ann. Int'l Conf. Computing and Combinatorics, pp. 276-286, http://www.springerlink.com/content/qr11k3075461263h/, 2008.
47. C. Zheng, Q. Zhu, Z. Adam, and D. Sankoff, "Guided Genome Halving: Hardness, Heuristics and the History of the Hemiascomycetes," Bioinformatics, vol. 24, no. 13, pp. i96-104, http://dx.doi.org/10.1093/ bioinformatics/btn146, 2008. (Pubitemid 351911662)
48. P. Feijão and J. Meidanis, "SCJ : A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy," WABI '09: Proc. Ninth Int'l Conf. Algorithms in Bioinformatics, pp. 85-96, 2009.
49. L.R. Foulds and R.L. Graham, "The Steiner Problem in Phylogeny is NP-Complete," Advances in Applied Math., vol. 3, pp. 43-49, 1982.
50. R. Warren and D. Sankoff, "Genome Halving with Double Cut and Join," J. Bioinformatics Computational Biology, vol. 7, no. 2, pp. 357-371, Apr. 2009