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

• Published in: Bioinformatics Vol. 22; no. 6; pp. 762 - 764
• Main Authors: Gerlach, Wolfgang, Giegerich, Robert
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.03.2006; Oxford Publishing Limited (England)
• Subjects: Algorithms; Base Pairing - genetics; Base Sequence; Dinucleoside Phosphates - genetics; Molecular Sequence Data; RNA - genetics; Sequence Alignment - methods; Sequence Analysis, RNA - methods; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btk041

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 Contact:robert@TechFak.Uni-Bielefeld.DE