Segmenting bacterial and viral DNA sequence alignments with a trans-dimensional phylogenetic factorial hidden Markov model

Lehrach, W.P. and Husmeier, D. (2009) Segmenting bacterial and viral DNA sequence alignments with a trans-dimensional phylogenetic factorial hidden Markov model. Journal of the Royal Statistical Society: Series C (Applied Statistics), 58(3), pp. 307-327. (doi:10.1111/j.1467-9876.2008.00648.x)

[img]
Preview
Text
69428.pdf

1MB

Abstract

The traditional approach to phylogenetic inference assumes that a single phylogenetic tree can represent the relationships and divergence between the taxa. However, taxa sequences exhibit varying levels of conservation, e.g. because of regulatory elements and active binding sites. Also, certain bacteria and viruses undergo interspecific recombination, where different strains exchange or transfer DNA subsequences, leading to a tree topology change. We propose a phylogenetic factorial hidden Markov model to detect recombination and rate variation simultaneously. This is applied to two DNA sequence alignments: one bacterial (Neisseria) and another of type 1 human immunodeficiency virus. Inference is carried out in the Bayesian framework, using reversible jump Markov chain Monte Carlo sampling.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Husmeier, Professor Dirk
Authors: Lehrach, W.P., and Husmeier, D.
College/School:College of Science and Engineering > School of Mathematics and Statistics > Statistics
Journal Name:Journal of the Royal Statistical Society: Series C (Applied Statistics)
Publisher:John Wiley & Sons Ltd
ISSN:0035-9254
Published Online:22 January 2009
Copyright Holders:Copyright © 2009 Royal Statistical Society
First Published:First published in Journal of the Royal Statistical Society: Series C (Applied Statistics) 58(3):307-327
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

University Staff: Request a correction | Enlighten Editors: Update this record