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Nucleic Acids Research 2005 33(7):2176-2180; doi:10.1093/nar/gki511
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Published online 14 April 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Masking repeats while clustering ESTs

Korbinian Schneeberger1, Ketil Malde2, Eivind Coward2,* and Inge Jonassen1,2

1Computational Biology Unit, University of Bergen Bergen, Norway 2Department of Informatics, University of Bergen Bergen, Norway

*To whom correspondence should be addressed. Tel: +47 55584068; Fax: +47 55584199; Email: coward{at}ii.uib.no

Received December 20, 2004. Revised March 10, 2005. Accepted March 28, 2005.

A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries. We present a fast and effective method that aims to eliminate the problems repeats cause in the process of clustering. Unlike traditional methods, repeats are inferred directly from the EST data, we do not rely on any external library of known repeats. This makes the method especially suitable for analysing the ESTs from organisms without good repeat libraries. We demonstrate that the result is very similar to performing standard repeat masking before clustering.


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