title: GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  GUUGle is available via the Bielefeld Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de/guugle
authors.affiliation: Faculty of Technology, Bielefeld University 33615 Bielefeld, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Gerlach
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
mesh_terms: D000465:Algorithms; D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D015226:Dinucleoside Phosphates / Q000235:genetics*; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D015226:Dinucleoside Phosphates; C018310:guanylyl-(3'-5')-uridine; D012313:RNA