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Bioinformatics Vol. 18 no. 2 2002
Pages 226-234
© 2002 Oxford University Press

A Bayesian approach to discriminate between alternative DNA sequence segmentations

Dirk Husmeier and Frank Wright

Biomathematics and Statistics Scotland (BioSS), SCRI, Invergowrie, Dundee DD2 5DA, UK

Received on March 26, 2001 ; revised on July 2, 2001 ; accepted on September 12, 2001

Motivation: As a result of recombination or rate variation, a DNA sequence alignment may have a mosaic structure, where different segments correspond to different evolutionary histories. While several methods have been developed to predict DNA mosaic structures, they do not properly address the question of whether the predicted segmentation itself is statistically significant, or whether it is significantly better than an alternative mosaic structure predicted with another method. The objective of the present article is to devise an approximate Bayesian hypothesis test to discriminate between alternative candidate mosaic structures.

Results: We have applied the proposed discrimination scheme to various synthetic and real-world DNA sequence alignments. On the synthetic data, the algorithm identified the true mosaic structure in nine out of ten cases. On the real-world sequence alignments, it selected the same mosaic structures as predicted in the literature.

Availability: Software written in MATLAB as well as the data sets used in our study are available from http://www.bioss.sari.ac.uk/~dirk/software/ABBESS/INFO.html.

Contact: dirk{at}bioss.ac.uk; frank{at}bioss.ac.uk


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