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

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. © 2006 Oxford University Press.