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Bioinformatics pp 385-416 | Cite as

Genome Rearrangement by the Double Cut and Join Operation

  • Richard Friedberg
  • Aaron E. Darling
  • Sophia Yancopoulos
Part of the Methods in Molecular Biology™ book series (MIMB, volume 452)

Abstract

The Double Cut and Join is an operation acting locally at four chromosomal positions without regard to chromosomal context. This chapter discusses its application and the resulting menu of operations for genomes consisting of arbitrary numbers of circular chromosomes, as well as for a general mix of linear and circular chromosomes. In the general case the menu includes: inversion, translocation, transposition, formation and absorption of circular intermediates, conversion between linear and circular chromosomes, block interchange, fission, and fusion. This chapter discusses the well-known edge graph and its dual, the adjacency graph, recently introduced by Bergeron et al. Step-by-step procedures are given for constructing and manipulating these graphs. Simple algorithms are given in the adjacency graph for computing the minimal DCJ distance between two genomes and finding a minimal sorting; and use of an online tool (Mauve) to generate synteny blocks and apply DCJ is described.

Key Words

Genome rearrangements gene order Mauve synteny inversion reversal transloca-tion transposition block interchange fission fusion 

Notes

Acknowledgments

The authors are grateful to David Sankoff for his advice and encouragement; Anne Bergeron for communicating the idea of the adjacency graph in advance of publication; Mike Tsai for his online implementation of the DCJ; and Betty Harris for invaluable logistic support and encouragement. S.Y. thanks Nicholas Chiorazzi for his enthusiasm, encouragement, and support; and A.E.D is supported by NSF grant DBI-0630765.

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Richard Friedberg
    • 1
  • Aaron E. Darling
    • 2
  • Sophia Yancopoulos
    • 3
  1. 1.Department of PhysicsColumbia UniversityNew York
  2. 2.ARC Centre of Excellence in Bioinformatics, and Institute for Molecular BioscienceThe University of QueenslandBrisbaneAustralia
  3. 3.The Feinstein Institute for Medical ResearchManhasset

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