On the inapproximability of the exemplar conserved interval distance problem of genomes

Journal of Combinatorial Optimization

Volumn 15, Issue 2, 2008, Pages 201-221

  Chen, Zhixiang ^a   Fowler, Richard H ^a   Fu, Bin ^a   Zhu, Binhai ^b  

^a UNIVERSITY OF TEXAS PAN AMERICAN   (United States)

^b Montana State University   (United States)

Author keywords

Approximation algorithm; Exemplar conserved interval distance; Genome rearrangement; Inapproximability; Weak approximation

Indexed keywords

APPROXIMATION ALGORITHMS; APPROXIMATION THEORY; POLYNOMIALS; PROBLEM SOLVING; THEOREM PROVING;

EXEMPLAR CONSERVED INTERVAL DISTANCE; GENOME REARRANGEMENT; WEAK APPROXIMATION;

GENES;

EID: 37749023210     PISSN: 13826905     EISSN: 15732886     Source Type: Journal    
DOI: 10.1007/s10878-007-9077-1     Document Type: Article

References (21)

1. Bafna V, Pevzner P (1995) Sorting by reversals: genome rearrangements in plant organelles and evolutionary history of X chromosome. Mol Biol Evol 12:239-246
2. Bereg S, Zhu B (2005) RNA multiple structural alignment with longest common subsequences. In: Proceedings of the 11th international annual confrerence on computers and combinatorics (COCOON'05). Lecture notes in computer science, vol 3595. Springer, Berlin, pp 32-41
3. Bergeron A, Stoye J (2003) On the similarity of sets of permutations and its applications to genome comparison. In: Proceedings of the 9th international annual confrerence on computers and combinatorics (COCOON'03). Lecture notes in computer science, vol 2697. Springer, Berlin, pp 68-79
4. Blin G, Rizzi R (2005) Conserved interval distance computation between non-trivial genomes. In: Proceedings of the 11th international annual confrerence on computers and combinatorics (COCOON'05). Lecture notes in computer science, vol 3595. Springer, Berlin, pp 22-31
5. Bryant D (2000) The complexity of calculating exemplar distances. In: Sankoff D, Nadeau J (eds) Comparative genomics: empirical and analytical approaches to gene order dynamics, map alignment, and the evolution of gene families. Kluwer Academic, Dordrecht, pp 207-212
6. Chen Z, Fowler RH, Fu B, Zhu B (2006a) Lowers bounds on the approximation of the conserved interval distance problem of genomes. In: Proceedings of the 12th international annual confrerence on computers and combinatorics (COCOON'06). Lecture notes in computer science, vol 4112. Springer, Berlin, pp 245-254
7. Chen Z, Fu B, Zhu B (2006b) The approximability of the exemplar breakpoint distance problem. In: Proceedings of the second international conference on algorithmic aspects in information and management (AAIM'06). Lecture notes in computer science, vol. 4041. Springer, Berlin, pp 291-302
8. Chen Z, Fu B, Xu J, Yang B, Zhao Z, Zhu B (2007) Non-breaking similarity of genomes with gene repetitions, submitted for publication. In: Proceedings of the 18th international symposium on combinatorial pattern matching (CPM'07). Lecture notes in computer science, vol 4580. Springer, Berlin, pp 119-130
9. Cormen T, Leiserson C, Rivest R, Stein C (2002) Introduction to algorithms, 2nd edn. McGraw-Hill, Cambridge
10. Garey M, Johnson D (1979) Computers and intractability: a guide to the theory of NP-completeness. Freeman, San Francisco
11. Gascuel O (ed) (2004) Mathematics of evolution and phylogeny. Oxford University Press, Oxford
12. Hannenhalli S, Pevzner P (1999) Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J ACM 46(1):1-27
13. Li Z, Wang L, Zhang K (2006) Algorithmic approaches for genome rearrangement: a review. IEEE Trans Sys Man Cybern Part C: Appl Rev 36(5):636-648
14. Makaroff C, Palmer J (1988) Mitochondrial DNA rearrangements and transcriptional alternatives in the male sterile cytoplasm of Ogura radish. Mol Cell Biol 8:1474-1480
15. Marron M, Swenson K, Moret B (2004) Genomic distances under deletions and insertions. Theor Comput Sci 325(3):347-360
16. Nguyen CT (2005) Algorithms for calculating exemplar distances. Honors thesis, School of Computing, National University of Singapore
17. Nguyen CT, Tay YC, Zhang L (2005) Divide-and-conquer approach for the exemplar breakpoint distance. Bioinformatics 21(10):2171-2176
18. Palmer J, Herbon L (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol 27:87-97
19. Sankoff D (1999) Genome rearrangement with gene families. Bioinformatics 16(11):909-917
20. Sturtevant A, Dobzhansky T (1936) Inversions in the third chromosome of wild races of drosophila pseudoobscura and their use in the study of the history of the species. Proc Natl Acad Sci USA 22:448-450
21. Watterson G, Ewens W, Hall T, Morgan A (1982) The chromosome inversion problem. J Theor Biol 99:1-7