Signed genome rearrangement by reversals and transpositions: Models and approximations?

Guo Hui Lin, Guoliang Xue

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

8 Scopus citations

Abstract

An important problem in computational molecular biology is the genome rearrangement using reversals and transpositions. Analysis of genome evolving by inversions and transpositions leads to a combina- torial optimization problem of sorting by reversals and transpositions, i.e., sorting of a permutation using reversals and transpositions of arbi- trary fragments. The reversal operation works on a single segment of the genome by reversing the selected segment. Two kinds of transpositions have been studied in the literature. The first kind of transposition oper- ation deletes a segment of the genome and insert it into another position in the genome. The second kind of transposition operation deletes a seg- ment of the genome and insert its inverse into another position in the genome. Both transposition operations can be viewed as operations work- ing on two consecutive segments. A third transposition operation working on two consecutive segments is introduced which, together with reversal and the first two kinds of transposition operations, forms the complete set of operations on two consecutive segments. In this paper, we study the sorting of a signed permutation by reversals and transpositions. By allowing only the first kind of transpositions, or the first two kinds of transpositions, or all three kinds of transpositions, we have three prob- lem models. After establishing a common lower bound on the numbers of operations needed, we present a unified 2-approximation algorithm for all these problems. Finally, we present a better 1:75-approximation for the third problem.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
PublisherSpringer Verlag
Pages71-80
Number of pages10
Volume1627
ISBN (Print)3540662006, 9783540662006
DOIs
StatePublished - 1999
Externally publishedYes
Event5th Annual International Conference on Computing and Combinatorics, COCOON 1999 - Tokyo, Japan
Duration: Jul 26 1999Jul 28 1999

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume1627
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other5th Annual International Conference on Computing and Combinatorics, COCOON 1999
CountryJapan
CityTokyo
Period7/26/997/28/99

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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  • Cite this

    Lin, G. H., & Xue, G. (1999). Signed genome rearrangement by reversals and transpositions: Models and approximations? In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 1627, pp. 71-80). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 1627). Springer Verlag. https://doi.org/10.1007/3-540-48686-0_7