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Detection of Homologous Recombination Events in Bacterial Genomes

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  • Wei-Bung Wang
  • Tao Jiang
  • Shea Gardner

Abstract

We study the detection of mutations, sequencing errors, and homologous recombination events (HREs) in a set of closely related microbial genomes. We base the model on single nucleotide polymorphisms (SNPs) and break the genomes into blocks to handle the rearrangement problem. Then we apply a dynamic programming algorithm to model whether changes within each block are likely a result of mutations, sequencing errors, or HREs. Results from simulation experiments show that we can detect 31%–61% of HREs and the precision of our detection is about 48%–90% depending on the rates of mutation and missing data. The HREfinder software for predicting HREs in a set of whole genomes is available as open source (http://sourceforge.net/projects/hrefinder/).

Suggested Citation

  • Wei-Bung Wang & Tao Jiang & Shea Gardner, 2013. "Detection of Homologous Recombination Events in Bacterial Genomes," PLOS ONE, Public Library of Science, vol. 8(10), pages 1-14, October.
    • Handle: RePEc:plo:pone00:0075230
    DOI: 10.1371/journal.pone.0075230
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