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

Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 762-764.

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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. AVAILABILITY: GUUGle is available via the Bielefeld Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de/guugle

@article{gerlach, 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. AVAILABILITY: GUUGle is available via the Bielefeld Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de/guugle}, address = {Faculty of Technology, Bielefeld University 33615 Bielefeld, Germany.}, author = {Gerlach, W. and Giegerich, R. }, citeulike-article-id = {705912}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {bioinformatics, motif, rna, search}, month = {March}, number = {6}, pages = {762--764}, posted-at = {2006-06-21 16:57:29}, priority = {2}, title = {GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16403789}, volume = {22}, year = {2006} }

RIS record

TY - JOUR ID - gerlach L3 - citeulike-article-id:705912 TI - GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. JF - Bioinformatics VL - 22 IS - 6 SP - 762 EP - 764 AD - Faculty of Technology, Bielefeld University 33615 Bielefeld, Germany. SN - 1367-4803 N2 - 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 KW - bioinformatics KW - motif KW - rna KW - search AU - Gerlach, W AU - Giegerich, R PY - 2006/03/15/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16403789 ER -

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