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)

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