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Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments

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Combinatorial Pattern Matching (CPM 2000)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1848))

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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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© 2000 Springer-Verlag Berlin Heidelberg

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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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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-67633-1

  • Online ISBN: 978-3-540-45123-5

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