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Bayesian modeling of recombination events in bacterial populations
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Marttinen, Pekka, Baldwin, Adam, Hanage, William P., Dowson, Christopher G. and Mahenthiralingam, Eshwar (2008) Bayesian modeling of recombination events in bacterial populations. BMC Bioinformatics, Vol.9 (No.421). doi:10.1186/1471-2105-9-421 ISSN 1471-2105.
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Official URL: http://dx.doi.org/10.1186/1471-2105-9-421
Abstract
Background: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of
strains in a data set increases.
Results: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the
corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites.
Conclusion: A multitude of challenging simulation scenarios and an analysis of real data from seven
housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities
offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/
mnf//mate/jc/software/brat.html.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QR Microbiology | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) > Biological Sciences ( -2010) | ||||
Library of Congress Subject Headings (LCSH): | Bayesian statistical decision theory, Bacteria, Evolution (biology) | ||||
Journal or Publication Title: | BMC Bioinformatics | ||||
Publisher: | BioMed Central Ltd. | ||||
ISSN: | 1471-2105 | ||||
Official Date: | 7 October 2008 | ||||
Dates: |
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Volume: | Vol.9 | ||||
Number: | No.421 | ||||
DOI: | 10.1186/1471-2105-9-421 | ||||
Status: | Peer Reviewed | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Funder: | ComMIT graduate school , Suomen Akatemia [Academy of Finland] |
Data sourced from Thomson Reuters' Web of Knowledge
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