GUUGle

Summary: GUUGle is a software tool that can efficiently locate potential helical regions under RNA base pairing rules, including Watson-Crick and G-U pairs. It takes a positive and a negative set of sequences and determines all exact matches between positive and negative sequences that exceed a specified length. The algorithm can also be adapted to use a precomputed suffix array of the positive sequence set. GUUGle can be used as a filter preceding more computationally expensive tasks such as miRNA target prediction.

Topic

Nucleic acid structure analysis

Detail

  • Operation: Sequence motif recognition;Sequence database search

  • Software interface: Web API;Web application;Command-line user interface

  • Language: C

  • License: Not stated

  • Cost: Free

  • Version name: 1.2

  • Credit: -

  • Input: -

  • Output: -

  • Contact: bibi-help@cebitec.uni-bielefeld.de

  • Collection: -

  • Maturity: -

Publications

  • GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.
  • Gerlach W and Giegerich R. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. 2006; 22:762-4. doi: 10.1093/bioinformatics/btk041
  • https://doi.org/10.1093/bioinformatics/btk041
  • PMID: 16403789
  • PMC: -

Download and documentation

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