An alignment-free test for recombination.
BACKGROUND
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.


METHODS
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/.
Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Institute for Neuro- and Bioinformatics, Lübeck University, 23562 Lübeck and Mathematical Stochastics, Mathematical Institute, Freiburg University, 79104 Freiburg, Germany.
Bernhard
B
Haubold
Linda
L
Krause
Thomas
T
Horn
Peter
P
Pfaffelhuber
D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D010802:Phylogeny; D011995:Recombination, Genetic; D016415:Sequence Alignment / Q000379:methods*