Multi-break rearrangements and chromosomal evolution

Theoretical Computer Science

Volumn 395, Issue 2-3, 2008, Pages 193-202

  Alekseyev, Max A ^a   Pevzner, Pavel A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Breakpoint graph; Genome rearrangement; Genomic distance; Multi break; Reversal; Translocation; Transposition

Indexed keywords

ADHESIVES; GLUES; THEOREM PROVING;

DUALITY THEOREMS; ELSEVIER (CO); EVOLUTION (CO); GENOME REARRANGEMENTS; POLYNOMIAL ALGORITHMS;

GLUING;

EID: 45849108363     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2008.01.013     Document Type: Article

References (40)

1. Ohno S. Evolution by Gene Duplication (1970), Springer, Berlin
2. Nadeau J.H., and Taylor B.A. Lengths of chromosomal segments conserved since divergence of man and mouse. Proceedings of the National Academy of Sciences 81 3 (1984) 814-818
3. Pevzner P.A., and Tesler G. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proceedings of the National Academy of Sciences 100 (2003) 7672-7677
4. Murphy W.J., Larkin D.M., van der Wind A.E., Bourque G., Tesler G., Auvil L., Beever J.E., Chowdhary B.P., Galibert F., Gatzke L., Hitte C., Meyers C.N., Milan D., Ostrander E.A., Pape G., Parker H.G., Raudsepp T., Rogatcheva M.B., Schook L.B., Skow L.C., Welge M., Womack J.E., O'Brien S.J., Pevzner P.A., and Lewin H.A. Dynamics of mammalian chromosome evolution inferred from multispecies comparative map. Science 309 5734 (2005) 613-617
5. van der Wind A.E., Kata S.R., Band M.R., Rebeiz M., Larkin D.M., Everts R.E., Green C.A., Liu L., Natarajan S., Goldammer T., Lee J.H., McKay S., Womack J.E., and Lewin H.A. A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Research 14 7 (2004) 1424-1437
6. Bailey J., Baertsch R., Kent W., Haussler D., and Eichler E. Hotspots of mammalian chromosomal evolution. Genome Biology 5 4 (2004) R23
7. Zhao S., Shetty J., Hou L., Delcher A., Zhu B., Osoegawa K., de Jong P., Nierman W.C., Strausberg R.L., and Fraser C.M. Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation. Genome Research 14 (2004) 1851-1860
8. Webber C., and Ponting C.P. Hotspots of mutation and breakage in dog and human chromosomes. Genome Research 15 12 (2005) 1787-1797
9. Hinsch H., and Hannenhalli S. Recurring genomic breaks in independent lineages support genomic fragility. BMC Evolutionary Biology 6 (2006) 90
10. Ruiz-Herrera A., Castresana J., and Robinson T.J. Is mammalian chromosomal evolution driven by regions of genome fragility?. Genome Biology 7 (2006) R115
11. D. Sankoff, P. Trinh, Chromosomal breakpoint re-use in the inference of genome sequence rearrangement, in: Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, RECOMB, 2004, pp. 30-35
12. Peng Q., Pevzner P.A., and Tesler G. The fragile breakage versus random breakage models of chromosome evolution. PLoS Computational Biology 2 (2006) e14
13. Sachs R.K., Levy D., and Hahnfeldt P. L. Hlatky, Quantitative analysis of radiation-induced chromosome aberrations. Cytogenetic and Genome Research 104 (2004) 142-148
14. Levy D., Vazquez M., Cornforth M., Loucas B., Sachs R.K., and Arsuaga J. Comparing DNA damage-processing pathways by computer analysis of chromosome painting data. Journal of Computational Biology 11 (2004) 626-641
15. Vazquez M., et al. Computer analysis of mFISH chromosome aberration data uncovers an excess of very complicated metaphases. International Journal of Radiation Biology 78 12 (2002) 1103-1115
16. Sachs R.K., Arsuaga J., Vazquez M., Hlatky L., and Hahnfeldt P. Using graph theory to describe and model chromosome aberrations. Radiation Research 158 (2002) 556-567
17. Alekseyev M.A., and Pevzner P.A. Are There Rearrangement Hotspots in the Human Genome?. PLoS Computational Biology 3 11 (2007) e209 10.1371/journal.pcbi.0030209
18. Bafna V., and Pevzner P.A. Genome rearrangement and sorting by reversals. SIAM Journal on Computing 25 (1996) 272-289
19. Pevzner P.A. Computational Molecular Biology: An Algorithmic Approach (2000), The MIT Press, Cambridge
20. Hannenhalli S., and Pevzner P. Transforming men into mouse (polynomial algorithm for genomic distance problem). Proceedings of the 36th Annual Symposium on Foundations of Computer Science (1995) 581-592
21. Tesler G. Efficient algorithms for multichromosomal genome rearrangements. Journal of Computer and System Sciences 65 (2002) 587-609
22. Ozery-Flato M., and Shamir R. Two notes on genome rearrangement. Journal of Bioinformatics and Computational Biology 1 (2003) 71-94
23. Yancopoulos S., Attie O., and Friedberg R. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21 (2005) 3340-3346
24. M.A. Alekseyev, P.A. Pevzner, Whole Genome Duplications, Multi-Break Rearrangements, and Genome Halving Theorem, in: Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA, 2007, pp. 665-679
25. Bafna V., and Pevzner P.A. Sorting permutations by transpositions. SIAM Journal on Discrete Mathematics 11 (1998) 224-240
26. D.A. Christie, Genome Rearrangement Problems, Ph.D. Thesis, University of Glasgow (1999)
27. Walter M.E., Reginaldo L., Curado A.F., and Oliveira A.G. Working on the problem of sorting by transpositions on genome rearrangements. Lecture Notes in Computer Science 2676 (2003) 372-383
28. Hartman T. A simpler 1.5-approximation algorithm for sorting by transpositions. Lecture Notes in Computer Science 2676 (2003) 156-169
29. Elias I., and Hartman T. A 1.375-approximation algorithm for sorting by transpositions. Lecture Notes in Computer Science 3692 (2005) 204-214
30. M. Bader, E. Ohlebusch, Sorting by weighted reversals, transpositions, and inverted transpositions, in: Proceedings of the 10th Conference on Research in Computational Molecular Biology, RECOMB, 2006, pp. 563-577
31. Gu Q.P., Peng S., and Sudborough H. A 2-approximation algorithm for genome rearrangements by reversals and transpositions. Theoretical Computer Science 210 (1999) 327-339
32. Hartman T., and Sharan R. A 1.5-approximation algorithm for sorting by transpositions and transreversals. Lecture Notes in Computer Science 3240 (2004) 50-61
33. Lin G.H., and Xue G. Signed genome rearrangements by reversals and transpositions: models and approximations. Theoretical Computer Science 259 (2001) 513-531
34. Lin Y.C., Lu C.L., Chang H.-Y., and Tang C.Y. An efficient algorithm for sorting by block-interchanges and its application to the evolution of vibrio species. Journal of Computational Biology 12 (2005) 102-112
35. Radcliffe A.J., Scott A.D., and Wilmer E.L. Reversals and transpositions over finite alphabets. SIAM Journal on Discrete Mathematics 19 (2005) 224-244
36. M.E. Walter, Z. Dias, J. Meidanis, Reversal and transposition distance of linear chromosomes, in: String Processing and Information Retrieval: A South American Symposium, SPIRE, 1998, pp. 96-102
37. Pasechnik D.V. On computing the Hilbert bases via the Elliott-MacMahon algorithm. Theoretical Computer Science 263 (2001) 37-46. http://stuwww.uvt.nl/ dpasech/software.html implementation:
38. Cox D., Little J., and O'Shea D. Ideals, Varieties, and Algorithms (1996), Springer-Verlag
39. G.-M. Greuel, G. Pfister, H. Schönemann, Singular 3.0.2. Website: http://www.singular.uni-kl.de
40. Alekseyev M.A. Multi-break rearrangements: from linear to circular genomes. Lecture Notes in Bioinformatics 4751 (2007) 1-15 10.1007/978-3-540-74960-8-1