STEINER POINTS IN THE SPACE OF GENOME REARRANGEMENTS

Author:

SANKOFF DAVID1,SUNDARAM GOPALAKRISHNAN2,KECECIOGLU JOHN3

Affiliation:

1. Centre de recherches mathématiques, Université de Montréal, CP 6128 succursale Centre-Ville, Montréal, Québec, H3C 3J7, Canada

2. Environmental Systems Research Institute, Redlands, CA 92373, USA

3. Department of Computer Science, University of Georgia, Athens, GA 30602, Greece

Abstract

We present some experiences with the problem of multiple genome comparison, analogous to multiple sequence alignment in sequence comparison, under the inversion and transposition distance metrics, given a fixed phylogeny. We first describe a heuristic for the case in which phylogeny is a star on three vertices and then use this to approximate the multiple genome comparison problem via local search.

Publisher

World Scientific Pub Co Pte Lt

Subject

Computer Science (miscellaneous)

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1. The distance and median problems in the single-cut-or-join model with single-gene duplications;Algorithms for Molecular Biology;2020-05-04

2. Bacterial phylogeny in the Cayley graph;Discrete Mathematics, Algorithms and Applications;2019-10

3. The Rooted SCJ Median with Single Gene Duplications;Comparative Genomics;2018

4. Median Approximations for Genomes Modeled as Matrices;Bulletin of Mathematical Biology;2016-04

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