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Bioinformatics Advance Access published online on October 11, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl519
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© 2006 The Author(s)
Received July 20, 2006
Revised September 12, 2006
Accepted October 6, 2006

Applications note

Repseek, a tool to retrieve approximate repeats from large DNA sequences

Guillaume Achaz 1 *, Frédéric Boyer 2, Eduardo P. C. Rocha 3, Alain Viari 2, and Eric Coissac 4

1 Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris 6, 12, rue Cuvier, 75005 Paris, France; UMR 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie-Paris6, Bâtiment A, 7, quai St Bernard, 75252 Paris Cedex 05, France
2 INRIA-Rhône Alpes projet HELIX, 655, avenue de l'Europe, Montbonnot, 38334 Saint Ismier Cedex, France
3 Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris 6, 12, rue Cuvier, 75005 Paris, France; Unité Génétique des Génomes Bactériens, Institut Pasteur, 28, rue du Dr. Roux, 75724 Paris Cedex 15, France
4 INRIA-Rhône Alpes projet HELIX, 655, avenue de l'Europe, Montbonnot, 38334 Saint Ismier Cedex, France; UMR 5163 LAPM, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France

* To whom correspondence should be addressed.
Guillaume Achaz, E-mail: achaz{at}abi.snv.jussieu.fr


  Abstract

Summary: Chromosomes or other long DNA sequences contain many highly similar repeated sub-sequences. While there are efficient methods for detecting strict repeats or detecting already characterized repeats, there is no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in a coherent statistical framework. Here, we present an implementation of a two-steps method (seed detection followed by their extension) that detects those approximate repeats. Our method is computationally efficient enough to handle large sequences and is flexible enough to account for influencing factors such as sequence-composition biases both at the seed detection and alignment levels.

Availability: http://wwwabi.snv.jussieu.fr/public/RepSeek/.

Associate Editor: John Quackenbush
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[Abstract] [Full Text] [PDF]


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