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An alignment-free test for recombination

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An alignment-free test for recombination. / Haubold, Bernhard; Krause, Linda; Horn, Thomas; Pfaffelhuber, Peter.

In: BIOINFORMATICS, Vol. 29, No. 24, 15.12.2013, p. 3121-7.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Haubold, B, Krause, L, Horn, T & Pfaffelhuber, P 2013, 'An alignment-free test for recombination', BIOINFORMATICS, vol. 29, no. 24, pp. 3121-7. https://doi.org/10.1093/bioinformatics/btt550

APA

Haubold, B., Krause, L., Horn, T., & Pfaffelhuber, P. (2013). An alignment-free test for recombination. BIOINFORMATICS, 29(24), 3121-7. https://doi.org/10.1093/bioinformatics/btt550

Vancouver

Haubold B, Krause L, Horn T, Pfaffelhuber P. An alignment-free test for recombination. BIOINFORMATICS. 2013 Dec 15;29(24):3121-7. https://doi.org/10.1093/bioinformatics/btt550

Bibtex

@article{4f75462cbc5f4903baa11c3c653026a3,
title = "An alignment-free test for recombination",
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 AND IMPLEMENTATION: 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/.",
keywords = "Algorithms, Computational Biology, Computer Simulation, Escherichia coli, Genome, Bacterial, Phylogeny, Recombination, Genetic, Sequence Alignment, Journal Article, Research Support, Non-U.S. Gov't",
author = "Bernhard Haubold and Linda Krause and Thomas Horn and Peter Pfaffelhuber",
year = "2013",
month = dec,
day = "15",
doi = "10.1093/bioinformatics/btt550",
language = "English",
volume = "29",
pages = "3121--7",
journal = "BIOINFORMATICS",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "24",

}

RIS

TY - JOUR

T1 - An alignment-free test for recombination

AU - Haubold, Bernhard

AU - Krause, Linda

AU - Horn, Thomas

AU - Pfaffelhuber, Peter

PY - 2013/12/15

Y1 - 2013/12/15

N2 - 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 AND IMPLEMENTATION: 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/.

AB - 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 AND IMPLEMENTATION: 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/.

KW - Algorithms

KW - Computational Biology

KW - Computer Simulation

KW - Escherichia coli

KW - Genome, Bacterial

KW - Phylogeny

KW - Recombination, Genetic

KW - Sequence Alignment

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1093/bioinformatics/btt550

DO - 10.1093/bioinformatics/btt550

M3 - SCORING: Journal article

C2 - 24064419

VL - 29

SP - 3121

EP - 3127

JO - BIOINFORMATICS

JF - BIOINFORMATICS

SN - 1367-4803

IS - 24

ER -