Hotel Estoril Eden, Monte Estoril,
Portugal
5-8 October 2005

 

 
 

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D
etecting Mosaic Structures in DNA Sequence Alignments

Dirk Husmeier
Biomathematics & Statistics Scotland (BioSS), UK

The objective of my talk is to discuss various statistical methods for detecting mosaic structures in bacterial and viral DNA sequence alignments. The challenge is to distinguish between interspecific recombination and rate heterogeneity. Interspecific recombination is a process that results in the transfer of DNA/RNA subsequences between different bacterial or viral strains. It constitutes an important source of genetic diversification in fast-evolving pathogens, like HIV-1, and has been identified as a possible cause for the emergence of multiple drug resistance in various bacterial genera, like Neisseria and Streptococcus.

Rate heterogeneity is a consequence of the fact that different regions of the genome are under different selective pressure, which results in a spatial variation of the nucleotide substitution rate or, more generally, the nucleotide substitution process parameters. The models and methods presented in my talk are based on the theory of Bayesian networks and Bayesian inference with Markov chain Monte Carlo.

After discussing several results obtained on a variety of bacterial and viral DNA sequence alignments, I will conclude with an outlook on other applications in functional genomics.