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CPM
2004
Springer

Sorting by Reversals in Subquadratic Time

9 years 6 months ago
Sorting by Reversals in Subquadratic Time
The problem of sorting a signed permutation by reversals is inspired by genome rearrangements in computational molecular biology. Given two genomes represented as two signed permutations of the same elements (e.g. orthologous genes), the problem consists in finding a most parsimonious scenario of reversals that transforms one genome into the other. We propose a method for sorting a signed permutation by reversals in time O(n n log n). The best known algorithms run in time O(n2 ), the main obstacle to an improvement being a costly operation of detection of so-called "safe" reversals. We bypass this detection and, using the same data structure as a previous random approximation algorithm, we achieve the same subquadratic complexity for finding an exact optimal solution. This answers an open question by Ozery-Flato and Shamir whether a subquadratic complexity could ever be achieved for solving the problem.
Eric Tannier, Marie-France Sagot
Added 20 Aug 2010
Updated 20 Aug 2010
Type Conference
Year 2004
Where CPM
Authors Eric Tannier, Marie-France Sagot
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