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
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
Authors: Jorge Vazquez-Anderson; Mia K Mihailovic; Kevin C Baldridge; Kristofer G Reyes; Katie Haning; Seung Hee Cho; Paul Amador; Warren B Powell; Lydia M Contreras Journal: Nucleic Acids Res Date: 2017-05-19 Impact factor: 16.971
Authors: Ferhat Alkan; Anne Wenzel; Oana Palasca; Peter Kerpedjiev; Anders Frost Rudebeck; Peter F Stadler; Ivo L Hofacker; Jan Gorodkin Journal: Nucleic Acids Res Date: 2017-05-05 Impact factor: 16.971
Authors: Cyrille Gavazzi; Matthieu Yver; Catherine Isel; Redmond P Smyth; Manuel Rosa-Calatrava; Bruno Lina; Vincent Moulès; Roland Marquet Journal: Proc Natl Acad Sci U S A Date: 2013-09-25 Impact factor: 11.205