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Bioinformatics Advance Access published online on January 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk041
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 21, 2005
Accepted January 4, 2006

Applications note

GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing

Wolfgang Gerlach 1 and Robert Giegerich 1 *

1 Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany

* To whom correspondence should be addressed.
Robert Giegerich, E-mail: robert{at}TechFak.Uni-Bielefeld.DE


  Abstract

Motivation: RNA secondary structure analysis often requires searching for potential helices in large sequence data.

Results: We present a utility program GUUGle that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a positive and a negative set of sequences, and determines all exact matches under RNA rules between positive and negative sequences that exceed a specified length. The GUUGle algorithm can also be adapted to use a precomputed suffix array of the positive sequence set. We show how this program can be effectively used as a filter preceding a more computationally expensive task such as miRNA target prediction.

Availability: GUUGle is available via the Bielefeld Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de/guugle.

Associate Editor: Martin Bishop
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