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  • Title: GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.
    Author: Gerlach W, Giegerich R.
    Journal: Bioinformatics; 2006 Mar 15; 22(6):762-4. PubMed ID: 16403789.
    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
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