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Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches

  • Tom Hartmann
  • Martin Middendorf
  • Matthias Bernt
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1704)

Abstract

Genome rearrangements are mutations that change the gene content of a genome or the arrangement of the genes on a genome. Several years of research on genome rearrangements have established different algorithmic approaches for solving some fundamental problems in comparative genomics based on gene order information. This review summarizes the literature on genome rearrangement analysis along two lines of research. The first line considers rearrangement models that are particularly well suited for a theoretical analysis. These models use rearrangement operations that cut chromosomes into fragments and then join the fragments into new chromosomes. The second line works with rearrangement models that reflect several biologically motivated constraints, e.g., the constraint that gene clusters have to be preserved. In this chapter, the border between algorithmically “easy” and “hard” rearrangement problems is sketched and a brief review is given on the available software tools for genome rearrangement analysis.

Key words

Gene order analysis Genome rearrangements Cut and join Gene cluster 

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© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Tom Hartmann
    • 1
  • Martin Middendorf
    • 1
  • Matthias Bernt
    • 1
  1. 1.Swarm Intelligence and Complex Systems GroupInstitute of Computer Science, University LeipzigLeipzigGermany

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