Abstract
Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. Following a series of work recently, Hannenhalli and Pevzner developed the first polynomial algorithm for the problem of sorting signed permutations by reversals and proposed an O(n 4) implementation of the algorithm. In this paper we exploit a few combinatorial properties of the cycle graph of a permutation and propose an O(n 2 α(n)) implementation of the algorithm where α is the inverse Ackerman function. Besides making this algorithm practical, our technique improves implementations of the other rearrangement distance problems.
This work is supported by NSF grant CCR9114545.
This work is supported by NSF Young Investigator Award, NIH grant 1R01 HG00987 and DOE grant DE-FG02-94ER61919.
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Berman, P., Hannenhalli, S. (1996). Fast sorting by reversal. In: Hirschberg, D., Myers, G. (eds) Combinatorial Pattern Matching. CPM 1996. Lecture Notes in Computer Science, vol 1075. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-61258-0_14
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DOI: https://doi.org/10.1007/3-540-61258-0_14
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