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
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Gerlach, WolfgangUniBi; Giegerich, RobertUniBi
Einrichtung
Centrum für Biotechnologie > Graduate Center
Centrum für Biotechnologie > Arbeitsgruppe R. Giegerich
Centrum für Biotechnologie > Institut für Bioinformatik
Technische Fakultät > AG Genominformatik
Technische Fakultät > AG Praktische Informatik
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. https://doi.org/10.1093/bioinformatics/btk041
Gerlach, Wolfgang, and Giegerich, Robert. 2006. “GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.”. Bioinformatics 22 (6): 762-764.
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.

23 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs.
King AM, Vanderpool CK, Degnan PH., mSphere 4(1), 2019
PMID: 30700509
Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools.
Antonov IV, Mazurov E, Borodovsky M, Medvedeva YA., Brief Bioinform 20(2), 2019
PMID: 29697742
ASSA: Fast identification of statistically significant interactions between long RNAs.
Antonov I, Marakhonov A, Zamkova M, Medvedeva Y., J Bioinform Comput Biol 16(1), 2018
PMID: 29375012
Inferring and analyzing module-specific lncRNA-mRNA causal regulatory networks in human cancer.
Zhang J, Le TD, Liu L, Li J., Brief Bioinform (), 2018
PMID: 29401217
Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates.
Pan X, Wenzel A, Jensen LJ, Gorodkin J., PLoS One 13(8), 2018
PMID: 30142196
A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.
Umu SU, Gardner PP., Bioinformatics 33(7), 2017
PMID: 27993777
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J., Nucleic Acids Res 45(8), 2017
PMID: 28108657
Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.
Vazquez-Anderson J, Mihailovic MK, Baldridge KC, Reyes KG, Haning K, Cho SH, Amador P, Powell WB, Contreras LM., Nucleic Acids Res 45(9), 2017
PMID: 28334800
Detecting RNA-RNA interactions in E. coli using a modified CLASH method.
Liu T, Zhang K, Xu S, Wang Z, Fu H, Tian B, Zheng X, Li W., BMC Genomics 18(1), 2017
PMID: 28468647
A comprehensive comparison of general RNA-RNA interaction prediction methods.
Lai D, Meyer IM., Nucleic Acids Res 44(7), 2016
PMID: 26673718
lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.
Hu R, Sun X., J Bioinform Comput Biol 14(4), 2016
PMID: 27306075
Predicting RNA secondary structures from sequence and probing data.
Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL., Methods 103(), 2016
PMID: 27064083
LncTar: a tool for predicting the RNA targets of long noncoding RNAs.
Li J, Ma W, Zeng P, Wang J, Geng B, Yang J, Cui Q., Brief Bioinform 16(5), 2015
PMID: 25524864
An assessment of bacterial small RNA target prediction programs.
Pain A, Ott A, Amine H, Rochat T, Bouloc P, Gautheret D., RNA Biol 12(5), 2015
PMID: 25760244
IRBIS: a systematic search for conserved complementarity.
Pervouchine DD., RNA 20(10), 2014
PMID: 25142064
A functional sequence-specific interaction between influenza A virus genomic RNA segments.
Gavazzi C, Yver M, Isel C, Smyth RP, Rosa-Calatrava M, Lina B, Moulès V, Marquet R., Proc Natl Acad Sci U S A 110(41), 2013
PMID: 24067651
Computational approaches to predicting the impact of novel bases on RNA structure and stability.
Harrison JG, Zheng YB, Beal PA, Tantillo DJ., ACS Chem Biol 8(11), 2013
PMID: 24063428
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.
Wenzel A, Akbasli E, Gorodkin J., Bioinformatics 28(21), 2012
PMID: 22923300
sTarPicker: a method for efficient prediction of bacterial sRNA targets based on a two-step model for hybridization.
Ying X, Cao Y, Wu J, Liu Q, Cha L, Li W., PLoS One 6(7), 2011
PMID: 21799937
Got target? Computational methods for microRNA target prediction and their extension.
Min H, Yoon S., Exp Mol Med 42(4), 2010
PMID: 20177143
Rapid match-searching for gene silencing assessment.
Horn ME, Waterhouse PM., Bioinformatics 26(16), 2010
PMID: 20601440
KnotSeeker: heuristic pseudoknot detection in long RNA sequences.
Sperschneider J, Datta A., RNA 14(4), 2008
PMID: 18314500
RNAplex: a fast tool for RNA-RNA interaction search.
Tafer H, Hofacker IL., Bioinformatics 24(22), 2008
PMID: 18434344

7 References

Daten bereitgestellt von Europe PubMed Central.

MicroRNA targets in Drosophila.
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS., Genome Biol. 5(1), 2003
PMID: 14709173

AUTHOR UNKNOWN, SOFTWARE PRACT EXP 33(), 2003
REPuter: the manifold applications of repeat analysis on a genomic scale.
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R., Nucleic Acids Res. 29(22), 2001
PMID: 11713313
Prediction of mammalian microRNA targets.
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB., Cell 115(7), 2003
PMID: 14697198
Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes.
Nicolas J, Durand P, Ranchy G, Tempel S, Valin AS., Bioinformatics 21(24), 2005
PMID: 16223791
Computational identification of microRNA targets.
Rajewsky N, Socci ND., Dev. Biol. 267(2), 2004
PMID: 15013811
Fast and effective prediction of microRNA/target duplexes.
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R., RNA 10(10), 2004
PMID: 15383676
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 16403789
PubMed | Europe PMC

Suchen in

Google Scholar