Introduction

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/).

Publications

  1. Detection of homologous recombination events in bacterial genomes.
    Cite this
    Wang WB, Jiang T, Gardner S, 2013-01-01 - PloS one

Credits

  1. Wei-Bung Wang
    Developer

    Department of Computer Science, University of California Riverside, United States of America

  2. Tao Jiang
    Developer

  3. Shea Gardner
    Investigator

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Summary
AccessionBT002021
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByShea Gardner