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Sorting Genomes with Insertions, Deletions and Duplications by DCJ

  • Sophia Yancopoulos
  • Richard Friedberg
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)

Abstract

We extend the DCJ paradigm to perform genome rearrangments on pairs of genomes having unequal gene content and/or multiple copies by permitting genes in one genome which are completely or partially unmatched in the other. The existence of unmatched gene ends introduces new kinds of paths in the adjacency graph, since some paths can now terminate internal to a chromosome and not on telomeres. We introduce Òghost adjacenciesÓ to supply the missing gene ends in the genome not containing them. Ghosts enable us to close paths that were due to incomplete matching, just as null points enable us to close even paths terminating in telomeres. We define generalalized DCJ operations on the generalized adjacency graph, and give a prescription for calculating the DCJ distance for the expanded repertoire of operations which includes insertions, deletions and duplications.

Keywords

Triangle Inequality Null Point Target Genome Adjacency Graph Circular Chromosome 
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 2008

Authors and Affiliations

  • Sophia Yancopoulos
    • 1
  • Richard Friedberg
    • 2
  1. 1.The Feinstein Institute for Medical ResearchManhassetUSA
  2. 2.Department of PhysicsColumbia UniversityNYUSA

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