Non-breaking similarity of genomes with gene repetitions

Zhixiang Chen, Bin Fu, Jinhui Xu, Boting Yang, Zhiyu Zhao, Binhai Zhu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

17 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages119-130
Number of pages12
Volume4580 LNCS
StatePublished - 2007
Event18th Annual Symposium on Combinatorial Pattern Matching, CPM 2007 - London, ON, Canada
Duration: Jul 9 2007Jul 11 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4580 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other18th Annual Symposium on Combinatorial Pattern Matching, CPM 2007
CountryCanada
CityLondon, ON
Period7/9/077/11/07

Fingerprint

Genome
Genes
Gene
Polynomials
Independent Set
Repetition
Similarity
Similarity Measure
Polynomial-time Algorithm
Polynomial time
Complement
Linearly
Approximation

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Chen, Z., Fu, B., Xu, J., Yang, B., Zhao, Z., & Zhu, B. (2007). Non-breaking similarity of genomes with gene repetitions. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 4580 LNCS, pp. 119-130). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4580 LNCS).

Non-breaking similarity of genomes with gene repetitions. / Chen, Zhixiang; Fu, Bin; Xu, Jinhui; Yang, Boting; Zhao, Zhiyu; Zhu, Binhai.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4580 LNCS 2007. p. 119-130 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4580 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chen, Z, Fu, B, Xu, J, Yang, B, Zhao, Z & Zhu, B 2007, Non-breaking similarity of genomes with gene repetitions. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 4580 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4580 LNCS, pp. 119-130, 18th Annual Symposium on Combinatorial Pattern Matching, CPM 2007, London, ON, Canada, 7/9/07.
Chen Z, Fu B, Xu J, Yang B, Zhao Z, Zhu B. Non-breaking similarity of genomes with gene repetitions. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4580 LNCS. 2007. p. 119-130. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Chen, Zhixiang ; Fu, Bin ; Xu, Jinhui ; Yang, Boting ; Zhao, Zhiyu ; Zhu, Binhai. / Non-breaking similarity of genomes with gene repetitions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4580 LNCS 2007. pp. 119-130 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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