TY - GEN

T1 - Non-breaking similarity of genomes with gene repetitions

AU - Chen, Zhixiang

AU - Fu, Bin

AU - Xu, Jinhui

AU - Yang, Boting

AU - Zhao, Zhiyu

AU - Zhu, Binhai

PY - 2007

Y1 - 2007

N2 - In this paper we define a new similarity measure, the non-breaking similarity, which is the complement of the famous breakpoint distance between genomes (in general, between any two sequences drawn from the same alphabet). When the two input genomes G and ℋ, drawn from the same set of n gene families, contain gene repetitions, we consider the corresponding Exemplar Non-breaking Similarity problem (ENbS) in which we need to delete repeated genes in G and ℋ such that the resulting genomes G and H have the maximum non-breaking similarity. We have the following results. - For the Exemplar Non-breaking Similarity problem, we prove that the Independent Set problem can be linearly reduced to this problem. Hence, ENbS does not admit any factor-n1-ε polynomial-time approximation unless P=NP. (Also, ENbS is W[1]-complete.) - We show that for several practically interesting cases of the Exemplar Non-breaking Similarity problem, there are polynomial time algorithms.

AB - In this paper we define a new similarity measure, the non-breaking similarity, which is the complement of the famous breakpoint distance between genomes (in general, between any two sequences drawn from the same alphabet). When the two input genomes G and ℋ, drawn from the same set of n gene families, contain gene repetitions, we consider the corresponding Exemplar Non-breaking Similarity problem (ENbS) in which we need to delete repeated genes in G and ℋ such that the resulting genomes G and H have the maximum non-breaking similarity. We have the following results. - For the Exemplar Non-breaking Similarity problem, we prove that the Independent Set problem can be linearly reduced to this problem. Hence, ENbS does not admit any factor-n1-ε polynomial-time approximation unless P=NP. (Also, ENbS is W[1]-complete.) - We show that for several practically interesting cases of the Exemplar Non-breaking Similarity problem, there are polynomial time algorithms.

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U2 - 10.1007/978-3-540-73437-6_14

DO - 10.1007/978-3-540-73437-6_14

M3 - Conference contribution

AN - SCOPUS:37749034336

SN - 9783540734369

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

SP - 119

EP - 130

BT - Combinatorial Pattern Matching - 18th Annual Symposium, CPM 2007, Proceedings

PB - Springer Verlag

T2 - 18th Annual Symposium on Combinatorial Pattern Matching, CPM 2007

Y2 - 9 July 2007 through 11 July 2007

ER -