A 1.5-approximation algorithm for sorting by transpositions and transreversals

Authors:
Tzvika Hartman;Roded Sharan
Affiliations:
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel;School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel
Venue:
Journal of Computer and System Sciences - Special issue on bioinformatics II
Year:
2005

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Abstract

One of the most promising ways to determine evolutionary distance between two organisms is to compare the order of appearance of orthologous genes in their genomes. The resulting genome rearrangement problem calls for finding a shortest sequence of rearrangement operations that sorts one genome into the other. In this paper we provide a 1.5-approximation algorithm for the problem of sorting by transpositions and transreversals, improving on a five-year-old 1.75 ratio for this problem. Our algorithm is also faster than current approaches and requires O(n^3^/^2logn) time for n genes.