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Bioinformatics Advance Access published online on July 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl368
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 19, 2006
Revised June 29, 2006
Accepted July 3, 2006

Article

RBR: library-less repeat detection for ESTs

Ketil Malde 1 *, Korbinian Schneeberger 2, Eivind Coward 3, and Inge Jonassen 4

1 Computational Biology Unit, Bergen Centre for Computational Sciences, University of Bergen
2 Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München
3 Department of Informatics, University of Bergen
4 Computational Biology Unit, Bergen Centre for Computational Sciences, University of Bergen; Department of Informatics, University of Bergen

* To whom correspondence should be addressed.
Ketil Malde, E-mail: ketil.malde{at}bccs.uib.no


  Abstract

Motivation: Repeat sequences in ESTs are a source of problems, in particular for clustering. ESTs are therefore commonly masked against a library of known repeats. High quality repeat libraries are available for the widely studied organisms, but for most other organisms the lack of such libraries is likely to compromise the quality of EST analysis.

Results: We present a fast, flexible, and library-less method for masking repeats in EST sequences, based on match statistics within the EST collection. The method is not linked to a particular clustering algorithm. Extensive testing on data sets using different clustering methods and a genomic mapping as reference shows that this method gives results that are better than or as good as those obtained using RepeatMasker with a repeat library.

Availability: The implementation of RBR is available under the terms of the GPL from http://www.ii.uib.no/~ketil/bioinformatics.

Associate Editor: Alex Bateman
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