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Detection of Homologous Recombination Events in Bacterial Genomes
- Wang, Wei-Bung;
- Jiang, Tao;
- Gardner, Shea
- Editor(s): Gibas, Cynthia
Published Web Location
https://doi.org/10.1371/journal.pone.0075230Abstract
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/).
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