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Finding All Sorting Tandem Duplication Random Loss Operations

  • Matthias Bernt
  • Ming-Chiang Chen
  • Daniel Merkle
  • Hung-Lung Wang
  • Kun-Mao Chao
  • Martin Middendorf
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5577)

Abstract

A tandem duplication random loss (TDRL) operation duplicates a contiguous segment of genes, followed by the loss of one copy of each of the duplicated genes. Although the importance of this operation is founded by several recent biological studies, it has been investigated only rarely from a theoretical point of view. Of particular interest are sorting TDRLs which are TDRLs that, when applied to a permutation representing a genome, reduce the distance towards another given permutation. The identification of sorting genome rearrangement operations in general is a key ingredient of many algorithms for reconstructing the evolutionary history of a set of species. In this paper we present methods to compute all sorting TDRLs for two given gene orders. In addition, a closed formula for the number of sorting TDRLs is derived and further properties of sorting TDRLs are investigated. It is also shown that the theoretical findings are useful for identifying unique sorting TDRL scenarios for mitochondrial gene orders.

Keywords

Gene Order Tandem Duplication Binary String Closed Formula Restricted Case 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Matthias Bernt
    • 1
  • Ming-Chiang Chen
    • 2
  • Daniel Merkle
    • 3
  • Hung-Lung Wang
    • 2
  • Kun-Mao Chao
    • 2
  • Martin Middendorf
    • 1
  1. 1.Parallel Computing and Complex Systems Group, Department of Computer ScienceUniversity of LeipzigGermany
  2. 2.Department of Computer Science and Information EngineeringNational Taiwan UniversityTaiwan
  3. 3.Department of Mathematics and Computer ScienceUniversity of Southern DenmarkOdenseDenmark

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