Abstract
Analysis of genome rearrangements allows to compare molecular data from species that diverged a very long time ago. Results and complexities are tightly related to the type of data and genome-level mutations considered. For sorted and signed data, Hannenhalli and Pevzner (HP) developed the first polynomial algorithm in the field. This algorithm solves the problem of sorting by reversals. In this paper, we show how to extend the HP approach to include insertions and deletions of gene segments, allowing to compare genomes containing different genes. We provide an exact algorithm for the asymmetric case, as applies in organellar genome evolution, and a heuristic for the symmetric case, with bounds and a diagnostic for determining whether the output is optimal.
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References
P. Berman and S. Hannenhalli. Fast sorting by reversals. In D. Hirschberg and G. Myers, editors, Combinatorial Pattern Matching, Proceedings of the 7th Annual Symposium, number 1075 in Lecture Notes in Computer Science, pages 168–185. Springer, 1996.
A. Caprara. Sorting by reversals is difficult. In Proceedings of the First Annual International Conference on Computational Molecular Biology (RE-COMB 97), pages 75–83, New York, 1997. ACM.
A. Caprara. Formulations and hardness of multiple sorting by reversals. In S. Istrail, P.A. Pevzner, and M.S. Waterman, editors, Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99), pages 84–93, New York, 1999. ACM.
S. Hannenhalli. Polynomial-time algorithm for computing translocation distance between genomes. In Z. Galil and E. Ukkonen, editors, Sixth Annual Symposium on Combinatorial Pattern Matching, volume 937 of Lecture Notes in Computer Science, pages 162–176, Berlin, 1995. Springer.
S. Hannenhalli and P.A. Pevzner. Transforming cabbage into turnip. (polynomial algorithm for sorting signed permutations by reversals). In Proceedings of the 27th Annual ACM-SIAM Symposium on the Theory of Computing, pages 178–189, 1995.
S. Hannenhalli and P.A. Pevzner. Transforming men into mice (polynomial algorithm for genomic distance problem). In Proceedings of the IEEE 36th Annual Symposium on Foundations of Computer Science, pages 581–592, 1995.
KLRB+98._M. Korab-Laskowska, P. Rioux, N. Brossard, TG. Littlejohn, MW. Gray, BF. Lang, and G. Burger. The organelle genome database project (gobase). Nucleic Acids Res, 26:139–146, 1998.
H. Kaplan, R. Shamir, and R.E. Tarjan. Faster and simpler algorithm for sorting signed permutations by reversals. In Proceedings of the 8th Annual ACM-SIAM Symposium on Discrete Algorithms, pages 344–351, New York, 1997.
Introduction to Computational Molecular Biology. PWS Publishing Company, 1997.
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El-Mabrouk, N. (2000). Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments. In: Giancarlo, R., Sankoff, D. (eds) Combinatorial Pattern Matching. CPM 2000. Lecture Notes in Computer Science, vol 1848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45123-4_20
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DOI: https://doi.org/10.1007/3-540-45123-4_20
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