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Bioinformatics. 2012 Sep 15;28(18):i402-i408. doi: 10.1093/bioinformatics/bts392.

Fractionation, rearrangement and subgenome dominance.

Author information

1
Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5. sankoff@uottawa.ca

Abstract

MOTIVATION:

Fractionation is arguably the greatest cause of gene order disruption following whole genome duplication, causing severe biases in chromosome rearrangement-based estimates of evolutionary divergence.

RESULTS:

We show how to correct for this bias almost entirely by means of a 'consolidation' algorithm for detecting and suitably transforming identifiable regions of fractionation. We characterize the process of fractionation and the performance of the algorithm through realistic simulations. We apply our method to a number of core eudicot genomes, we and by studying the fractionation regions detected, are able to address topical issues in polyploid evolution.

AVAILABILITY AND IMPLEMENTATION:

Code for the consolidation algorithm, and sample data, is available at: http://137.122.149.195/Software/Fractionation/fractionation.html

CONTACT:

sankoff@uottawa.ca.

PMID:
22962459
PMCID:
PMC3436819
DOI:
10.1093/bioinformatics/bts392
[Indexed for MEDLINE]
Free PMC Article
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