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

Gerlach W, Giegerich R (2006)
Bioinformatics 22(6): 762-764.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
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.
Stichworte
bioinformatics motif rna search
Erscheinungsjahr
2006
Zeitschriftentitel
Bioinformatics
Band
22
Ausgabe
6
Seite(n)
762-764
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1902179

Zitieren

Gerlach W, Giegerich R. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics. 2006;22(6):762-764.
Gerlach, W., & Giegerich, R. (2006). GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics, 22(6), 762-764. doi:10.1093/bioinformatics/btk041
Gerlach, W., and Giegerich, R. (2006). GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics 22, 762-764.
Gerlach, W., & Giegerich, R., 2006. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics, 22(6), p 762-764.
W. Gerlach and R. Giegerich, “GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.”, Bioinformatics, vol. 22, 2006, pp. 762-764.
Gerlach, W., Giegerich, R.: GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing. Bioinformatics. 22, 762-764 (2006).
Gerlach, Wolfgang, and Giegerich, Robert. “GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.”. Bioinformatics 22.6 (2006): 762-764.

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