IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0075230.html
   My bibliography  Save this article

Detection of Homologous Recombination Events in Bacterial Genomes

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075230
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0075230&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0075230?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Antonis Rokas & Barry L. Williams & Nicole King & Sean B. Carroll, 2003. "Genome-scale approaches to resolving incongruence in molecular phylogenies," Nature, Nature, vol. 425(6960), pages 798-804, October.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Wang Yuancheng & Degnan James H, 2011. "Performance of Matrix Representation with Parsimony for Inferring Species from Gene Trees," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-39, May.
    2. Martín Espariz & Federico A Zuljan & Luis Esteban & Christian Magni, 2016. "Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case," PLOS ONE, Public Library of Science, vol. 11(9), pages 1-17, September.
    3. Rahul Siddharthan & Eric D Siggia & Erik van Nimwegen, 2005. "PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny," PLOS Computational Biology, Public Library of Science, vol. 1(7), pages 1-23, December.
    4. Roch, Sebastien & Steel, Mike, 2015. "Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent," Theoretical Population Biology, Elsevier, vol. 100(C), pages 56-62.
    5. David Peris & Emily J. Ubbelohde & Meihua Christina Kuang & Jacek Kominek & Quinn K. Langdon & Marie Adams & Justin A. Koshalek & Amanda Beth Hulfachor & Dana A. Opulente & David J. Hall & Katie Hyma , 2023. "Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    6. Haque Md Rejuan & Kubatko Laura, 2024. "A global test of hybrid ancestry from genome-scale data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 23(1), pages 1-18, January.
    7. Alexei J Drummond & Simon Y W Ho & Matthew J Phillips & Andrew Rambaut, 2006. "Relaxed Phylogenetics and Dating with Confidence," PLOS Biology, Public Library of Science, vol. 4(5), pages 1-1, March.
    8. Sergio Consoli & Jan Korst & Steffen Pauws & Gijs Geleijnse, 2020. "Improved metaheuristics for the quartet method of hierarchical clustering," Journal of Global Optimization, Springer, vol. 78(2), pages 241-270, October.
    9. Cuong Than & Luay Nakhleh, 2009. "Species Tree Inference by Minimizing Deep Coalescences," PLOS Computational Biology, Public Library of Science, vol. 5(9), pages 1-12, September.
    10. Siewert Elizabeth A & Kechris Katerina J, 2009. "Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-36, September.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0075230. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.