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Bioinformatics Advance Access originally published online on April 1, 2008
Bioinformatics 2008 24(11):1332-1338; doi:10.1093/bioinformatics/btn111
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Expected gene-order distances and model selection in bacteria

Daniel Dalevi 1 and Niklas Eriksen 2,*

1Department of Computing Science and Engineering, Chalmers University of Technology, SE-412 96 Göteborg and 2Department of Mathematical Sciences, Göteborg University and Chalmers University of Technology,SE-412 96 Göteborg, Sweden

*To whom correspondence should be addressed.


  Abstract

Motivation: The evolutionary distance inferred from gene-order comparisons of related bacteria is dependent on the model. Therefore, it is highly important to establish reliable assumptions before inferring its magnitude.

Results: We investigate the patterns of dotplots between species of bacteria with the purpose of model selection in gene-order problems. We find several categories of data which can be explained by carefully weighing the contributions of reversals, transpositions, symmetrical reversals, single gene transpositions and single gene reversals. We also derive method of moments distance estimates for some previously uncomputed cases, such as symmetrical reversals, single gene reversals and their combinations, as well as the single gene transpositions edit distance.

Contact: ner{at}math.chalmers.se

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on October 25, 2007; revised on March 25, 2008; accepted on March 27, 2008

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