Detection of homologous recombination events in bacterial genomes.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 24116030.
- Also identified by DOI 10.1371/journal.pone.0075230 and PMC identifier 3792089.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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/).
Medical subject headings
- Genome, Bacterial
- Genomics
- Homologous Recombination