TY - GEN

T1 - A randomized FPT approximation algorithm for maximum alternating-cycle decomposition with applications

AU - Jiang, Haitao

AU - Pu, Lianrong

AU - Qingge, Letu

AU - Sankoff, David

AU - Zhu, Binhai

N1 - Publisher Copyright:
© 2018, Springer International Publishing AG, part of Springer Nature.

PY - 2018

Y1 - 2018

N2 - Comparing genomes in terms of gene order is a classical combinatorial optimization problem in computational biology. Some of the popular distances include translocation, reversal, and double-cut-and-join (abbreviated as DCJ), which have been extensively used while comparing two genomes. Let (Formula Presented) {translocation, reversal, DCJ}, be the distance between two genomes such that one can be sorted/converted into the other using the minimum number of x-operations. All these problems are NP-hard when the genomes are unsigned. Computing (Formula Presented) {translocation, reversal, DCJ}, between two unsigned genomes involves computing a proper alternating cycle decomposition of its breakpoint graph, which becomes the bottleneck for computing the genomic distance under almost all types of genome rearrangement operations and prohibits to obtain approximation factors better than 1.375 in polynomial time. In this paper, we devise an FPT (fixed-parameter tractable) approximation algorithm for computing the DCJ and translocation distances with an approximation factor 4/3+ ε, and the running time is (Formula Presented), where (Formula Presented) represents the optimal DCJ or translocation distance. The algorithm is randomized and it succeeds with a high probability. This technique is based on a new randomized method to generate approximate maximum alternating cycle decomposition.

AB - Comparing genomes in terms of gene order is a classical combinatorial optimization problem in computational biology. Some of the popular distances include translocation, reversal, and double-cut-and-join (abbreviated as DCJ), which have been extensively used while comparing two genomes. Let (Formula Presented) {translocation, reversal, DCJ}, be the distance between two genomes such that one can be sorted/converted into the other using the minimum number of x-operations. All these problems are NP-hard when the genomes are unsigned. Computing (Formula Presented) {translocation, reversal, DCJ}, between two unsigned genomes involves computing a proper alternating cycle decomposition of its breakpoint graph, which becomes the bottleneck for computing the genomic distance under almost all types of genome rearrangement operations and prohibits to obtain approximation factors better than 1.375 in polynomial time. In this paper, we devise an FPT (fixed-parameter tractable) approximation algorithm for computing the DCJ and translocation distances with an approximation factor 4/3+ ε, and the running time is (Formula Presented), where (Formula Presented) represents the optimal DCJ or translocation distance. The algorithm is randomized and it succeeds with a high probability. This technique is based on a new randomized method to generate approximate maximum alternating cycle decomposition.

UR - http://www.scopus.com/inward/record.url?scp=85049685251&partnerID=8YFLogxK

U2 - 10.1007/978-3-319-94776-1_3

DO - 10.1007/978-3-319-94776-1_3

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AN - SCOPUS:85049685251

SN - 9783319947754

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 26

EP - 38

BT - Computing and Combinatorics - 24th International Conference, COCOON 2018, Proceedings

A2 - Zhu, Daming

A2 - Wang, Lusheng

PB - Springer Verlag

T2 - 24th International Conference on Computing and Combinatorics Conference, COCOON 2018

Y2 - 2 July 2018 through 4 July 2018

ER -