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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 Arbitrary Strings

Distances between Arbitrary Strings

Chapter:
(p.97) 8 Distances between Arbitrary Strings
Source:
Combinatorics of Genome Rearrangements
Author(s):

Guillaume Fertin

Anthony Labarre

Irena Rusu

Eric Tannier

Steéphane Vialette

Publisher:
The MIT Press
DOI:10.7551/mitpress/9780262062824.003.0008

This chapter presents two main ideas to deal with arbitrary (that is, not necessarily balanced) strings. The first idea aims to transform strings into permutations, using the match-and-prune model in order to minimize the distance or maximize the similarity between the resulting permutations. Section 8.1 presents this model. The second idea is based on counting the number of operations needed to transform one string into another. Inserting, duplicating, replacing, or deleting a character or, more generally, a substring are operations that allow us to change the content of a string as needed. This is subsequently called the block edit model, which is surveyed in Section 8.2.

Keywords:   match-and-prune model, permutations, block edit model, arbitrary strings

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