An alignment-free test for recombination

Haubold, Bernhard; Krause, Linda; Horn, Thomas; Pfaffelhuber, Peter

doi:10.1093/bioinformatics/btt550

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An alignment-free test for recombination

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Haubold, Bernhard
Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Krause, Linda
Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Haubold, B., Krause, L., Horn, T., & Pfaffelhuber, P. (2013). An alignment-free test for recombination. Bioinformatics, 29(24), 3121-3127. doi:10.1093/bioinformatics/btt550.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0014-64A6-D

Abstract

Motivation: Why recombination? is one of the central questions in biology. This has led to a host of methods for quantifying recombination from sequence data. These methods are usually based on aligned DNA sequences. Here we propose an efficient alignment-free alternative. Results: Our method is based on the distribution of match lengths, which we look up using enhanced suffix arrays. By eliminating the alignment step, the test becomes fast enough for application to whole bacterial genomes. Using simulations we show that our test has similar power as established tests when applied to long pairs of sequences. When applied to 58 genomes of Escherichia coli, we pick up the strongest recombination signal from a 125 kb horizontal gene transfer engineered 20 years ago. Availability: We have implemented our method in the command-line program rush. Its C sources and documentation are available under the GNU General Public License from http://guanine.evolbio.mpg.de/rush/ Contact: haubold@evolbio.mpg.de