A linear time algorithm for the inversion median problem in circular bacterial genomes

Journal of Discrete Algorithms

Volumn 5, Issue 4 SPEC. ISS., 2007, Pages 637-646

  Ohlebusch, Enno ^a   Abouelhoda, Mohamed I ^a   Hockel, Kathrin ^a  

^a UNIVERSITY OF ULM   (Germany)

Author keywords

Circular genomes; Comparative genomics; Genome rearrangements; Inversions; Median problem; Reversal distance

Indexed keywords

BACTERIA; CONSTRAINT THEORY; GENES; INVERSE PROBLEMS; PROBLEM SOLVING; TREES (MATHEMATICS);

CIRCULAR GENOMES; COMPARATIVE GENOMICS; GENOME REARRANGEMENTS; INVERSIONS; MEDIAN PROBLEMS; REVERSAL DISTANCE;

ALGORITHMS;

EID: 35348856326     PISSN: 15708667     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jda.2006.12.006     Document Type: Article

References (25)

1. Bader D.A., Moret B.M.E., and Yan M. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. Journal of Computational Biology 8 (2001) 483-491
2. Bergeron A., Mixtacki J., and Stoye J. Reversal distance without hurdles and fortresses. Proc. 15th Annual Symposium on Combinatorial Pattern Matching. Lecture Notes in Computer Science vol. 3109 (2004), Springer-Verlag, Berlin 388-399
3. Blanchette M., Bourque G., and Sankoff D. Breakpoint phylogenies. Proc. Genome Informatics Workshop (1997), Univ. Academy Press 25-34
4. Bourque B., and Pevzner P.A. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Research 12 1 (2002) 26-36
5. Caprara A. Formulations and hardness of multiple sorting by reversals. Proc. 3rd Annual International Conference on Research in Computational Molecular Biology (1999), ACM Press, New York 84-94
6. Caprara A. On the practical solution of the reversal median problem. Proc. 1st International Workshop on Algorithms in Bioinformatics. Lecture Notes in Computer Science vol. 2149 (2001), Springer-Verlag, Berlin 238-251
7. Dalevi D.A., Eriksen N., Eriksson K., and Andersson S.G.E. Measuring genome divergence in bacteria: A case study using chlamydian data. Journal of Molecular Evolution 55 (2002) 24-36
8. Dobzhansky T., and Sturtevant A.H. Inversions in the chromosomes of Drosophila pseudoobscura. Genetics 23 (1938) 28-64
9. Eisen J.A., Heidelberg J.F., White O., and Salzberg S.L. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 1 6 (2000) 1-9
10. Hannenhalli S., and Pevzner P.A. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Journal of the ACM 48 (1999) 1-27
11. Hartman T., and Sharan R. A 1.5-approximation algorithm for sorting by transpositions and transreversals. Proc. of 4th International Workshop on Algorithms in Bioinformatics. Lecture Notes in Computer Science vol. 3240 (2004), Springer-Verlag, Berlin 50-61
12. Hughes D. Evaluating genome dynamics: The constraints on rearrangements within bacterial genomes. Genome Biology 1 6 (2000) 1-8
13. Kaplan H., Shamir R., and Tarjan R.E. A faster and simpler algorithm for sorting signed permutations by reversals. SIAM Journal on Computing 29 3 (1999) 880-892
14. Lefebvre J.F., El-Mabrouk N., Tillier E.R.M., and Sankoff D. Detection and validation of single gene inversions. Bioinformatics 19 (2003) i190-i196
15. Mackiewicz P., Mackiewicz D., Kowalczuk M., and Cebrat S. Flip-flop around the origin and terminus of replication in prokaryotic genomes. Genome Biology 2 12 (2001) 1-4
16. Moret B.M.E., Siepel A.C., Tang J., and Liu T. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. Proc. 2nd International Workshop on Algorithms in Bioinformatics. Lecture Notes in Computer Science vol. 2542 (2002), Springer-Verlag, Berlin 521-536
17. 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 of the United States of America 81 3 (1984) 814-818
18. Ohlebusch E., Abouelhoda M.I., Hockel K., and Stallkamp J. The median problem for the reversal distance in circular bacterial genomes. Proc. 16th Annual Symposium on Combinatorial Pattern Matching. Lecture Notes in Computer Science vol. 3537 (2005), Springer-Verlag, Berlin 116-127
19. I. Pe'er, R. Shamir, The median problems for breakpoints are NP-complete, Technical Report TR98-071, Electronic Colloquium on Computational Complexity, 1998
20. Sankoff D. Edit distance for genome comparison based on non-local operations. Proc. 3rd Annual Symposium on Combinatorial Pattern Matching, 3rd Annual Symposium. Lecture Notes in Computer Science vol. 644 (1992), Springer-Verlag, Berlin 121-135
21. Sankoff D., and Blanchette M. Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology 5 3 (1998) 555-570
22. Siepel A.C., and Moret B.M.E. Finding an optimal inversion median: Experimental results. Proc. 1st International Workshop on Algorithms in Bioinformatics. Lecture Notes in Computer Science vol. 2149 (2001), Springer-Verlag, Berlin 189-203
23. Suyama M., and Bork P. Evolution of prokaryotic gene order: Genome rearrangement in closely related species. TRENDS in Genetics 17 1 (2001) 10-13
24. Tiller E.R.M., and Collins R. Genome rearrangement by replication-directed translocation. Nature Genetics 26 (2000) 195-197
25. Watterson G.A., Ewens W.J., Hall T.E., and Morgan A. The chromosome inversion problem. Journal of Theoretical Biology 99 (1982) 1-7