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Bioinformatics Advance Access published online on September 23, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti040
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 18, 2004
Revised July 29, 2004
Accepted August 3, 2004

Article

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 20057, USA

* To whom correspondence should be addressed. E-mail: jgraham{at}stat.sfu.ca.


  Abstract

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

Results: We illustrate the approach by analyses of a simulated data set and alignments of real data from HIV-1 and human chromosome 7. Simulation results are presented which compare the statistical properties of one- 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 found come 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-square method, tested with the gcc compiler on Linux and WindowsXP, is available at http://stat-db.stat.sfu.ca/stepwise/.


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