Elsevier

Theoretical Computer Science

Volume 410, Issue 51, 28 November 2009, Pages 5300-5316
Theoretical Computer Science

A new linear time algorithm to compute the genomic distance via the double cut and join distance

https://doi.org/10.1016/j.tcs.2009.09.008Get rights and content
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Abstract

The genomic distance problem in the Hannenhalli–Pevzner (HP) theory is the following: Given two genomes whose chromosomes are linear, calculate the minimum number of translocations, fusions, fissions and inversions that transform one genome into the other. This paper presents a new distance formula based on a simple tree structure that captures all the delicate features of this problem in a unifying way, and a linear time algorithm for computing this distance.

Keywords

Comparative genomics
Genome rearrangements
Genomic distance computation
Sorting by translocations, fusions, fissions and inversions

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