GUUGle is a utility for fast exact matching under RNA base pairing rules.RNA secondary structure analysis often requires searching for potential helices in large sequence data. 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 target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.
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GUUGle: A utility for fast exact matching under RNA base pairing rules
W. Gerlach, R. Giegerich
in Bioinformatics, 22(6), Pages:762-764, 2006