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要旨:
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
