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Combinatorics of Genome Rearrangements$
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Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Stéphane Vialette

Print publication date: 2009

Print ISBN-13: 9780262062824

Published to MIT Press Scholarship Online: August 2013

DOI: 10.7551/mitpress/9780262062824.001.0001

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Distances between Signed Permutations

Distances between Signed Permutations

(p.63) 4 Distances between Signed Permutations
Combinatorics of Genome Rearrangements

Guillaume Fertin

Anthony Labarre

Irena Rusu

Eric Tannier

Steéphane Vialette

The MIT Press

Signed permutations allow the relative orientation of homologous markers to be taken into account and constitute a more biologically relevant model for genomes. Reversals, for instance, always change the strand of the reversed segment, so that the orientation of a gene inside the segment is also changed. Thus, whenever the orientation of genes is known and mutations that affect orientations are considered, it is better to use signed permutations as a model. This chapter discusses conserved interval distance; signed reversal distance; variants of sorting by reversals; combined operations; and double cut-and-joins.

Keywords:   homologous markers, genomes, signed permutations, interval distance, reversal distance, double cut-and-joins

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