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Bioinformatics Advance Access originally published online on September 23, 2004
Bioinformatics 2005 21(5):589-595; doi:10.1093/bioinformatics/bti040
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Stepwise detection of recombination breakpoints in sequence alignments

Jinko Graham 1,*, Brad McNeney 1 and Françoise Seillier-Moiseiwitsch 2

1 Department of Statistics and Actuarial Science, Simon Fraser University Burnaby, Canada V5A 1S6
2 Division of Biostatistics and Bioinformatics, Lombardi Cancer Center, Georgetown University Washington, DC, WA 20057, USA

*To whom correspondence should be addressed.

Motivation: We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints.

Results: We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected.

Availability: A makefile and C source code for phylogenetic profiling and the maximum {chi}2 method, tested with the gcc compiler on Linux and WindowsXP, are available at http://stat-db.stat.sfu.ca/stepwise/

Contact: jgraham{at}stat.sfu.ca


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