ArticlePloS one2013
Detection of homologous recombination events in bacterial genomes.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics.The Plant cell · 2021Article
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Authors and funding
3 authors.
Funding
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/).
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Registered trials
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