An O(n(3)) algorithm for sorting signed genomes by reversals, transpositions, transreversals and block-interchanges

作者：Yu, Shuzhi^*; Hao, Fanchang^*; Leong, Hon Wai^*

来源：Journal of Bioinformatics and Computational Biology, 2016, 14(1): 1640002.

DOI：10.1142/S0219720016400023

• Algorithm
• genome rearrangement
• genome sorting
• approximation algorithm
• reversal
• transreversal
• transposition
• block-interchange

We consider the problem of sorting signed permutations by reversals, transpositions, transreversals, and block-interchanges. The problem arises in the study of species evolution via large-scale genome rearrangement operations. Recently, Hao et al. gave a 2-approximation scheme called genome sorting by bridges (GSB) for solving this problem. Their result extended and unified the results of (i) He and Chen - a 2-approximation algorithm allowing reversals, transpositions, and block-interchanges (by also allowing transversals) and (ii) Hartman and Sharan - a 1.5-approximation algorithm allowing reversals, transpositions, and transversals (by also allowing block-interchanges). The GSB result is based on introduction of three bridge structures in the breakpoint graph, the L-bridge, T-bridge, and X-bridge that models good-reversal, transposition/transreversal, and block-interchange, respectively. However, the paper by Hao et al. focused on proving the 2-approximation GSB scheme and only mention a straightforward O(n(6)) algorithm. In this paper, we give an O(n(3)) algorithm for implementing the GSB scheme. The key idea behind our faster GSB algorithm is to represent cycles in the breakpoint graph by their canonical sequences, which greatly simplifies the search for these bridge structures. We also give some comparison results (running time and computed distances) against the original GSB implementation.

• 出版日期2016-2
• 单位山东大学; 山东政法学院