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Bioinformatics Advance Access originally published online on January 10, 2006
Bioinformatics 2006 22(6):762-764; doi:10.1093/bioinformatics/btk041
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GUUGle: a utility for fast exact matching under RNA complementary rules including G–U base pairing

Wolfgang Gerlach and Robert Giegerich *

Faculty of Technology, Bielefeld University 33615 Bielefeld, Germany

*To whom correspondence should be addressed.

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

Contact: robert{at}TechFak.Uni-Bielefeld.DE

Received on December 21, 2005; revised on January 4, 2006; accepted on January 4, 2006

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