pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
Reeder J, Steffen P, Giegerich R (2007)
NUCLEIC ACIDS RESEARCH 35(Web Server): W320-W324.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Reeder, Jens;
Steffen, PeterUniBi;
Giegerich, RobertUniBi
Einrichtung
Abstract / Bemerkung
RNA pseudoknots are an important structural feature of RNAs, but often neglected in computer predictions for reasons of efficiency. Here, we present the pknotsRG Web Server for single sequence RNA secondary structure prediction including pseudoknots. pknotsRG employs the newest Turner energy rules for finding the structure of minimal free energy. The algorithm has been improved in several ways recently. First, it has been reimplemented in the C programming language, resulting in a 60-fold increase in speed. Second, all suboptimal foldings up to a user-defined threshold can be enumerated. For large scale analysis, a fast sliding window mode is available. Further improvements of the Web Server are a new output visualization using the PseudoViewer Web Service or RNAmovies for a movie like animation of several suboptimal foldings. The tool is available as source code, binary executable, online tool or as Web Service. The latter alternative allows for an easy integration into bio-informatics pipelines. pknotsRG is available at the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/pknotsrg).
Erscheinungsjahr
2007
Zeitschriftentitel
NUCLEIC ACIDS RESEARCH
Band
35
Ausgabe
Web Server
Seite(n)
W320-W324
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/1587974
Zitieren
Reeder J, Steffen P, Giegerich R. pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. NUCLEIC ACIDS RESEARCH. 2007;35(Web Server):W320-W324.
Reeder, J., Steffen, P., & Giegerich, R. (2007). pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. NUCLEIC ACIDS RESEARCH, 35(Web Server), W320-W324. https://doi.org/10.1093/nar/gkm258
Reeder, Jens, Steffen, Peter, and Giegerich, Robert. 2007. “pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows”. NUCLEIC ACIDS RESEARCH 35 (Web Server): W320-W324.
Reeder, J., Steffen, P., and Giegerich, R. (2007). pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. NUCLEIC ACIDS RESEARCH 35, W320-W324.
Reeder, J., Steffen, P., & Giegerich, R., 2007. pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. NUCLEIC ACIDS RESEARCH, 35(Web Server), p W320-W324.
J. Reeder, P. Steffen, and R. Giegerich, “pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows”, NUCLEIC ACIDS RESEARCH, vol. 35, 2007, pp. W320-W324.
Reeder, J., Steffen, P., Giegerich, R.: pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. NUCLEIC ACIDS RESEARCH. 35, W320-W324 (2007).
Reeder, Jens, Steffen, Peter, and Giegerich, Robert. “pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows”. NUCLEIC ACIDS RESEARCH 35.Web Server (2007): W320-W324.
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Reeder J, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15294028
Reeder J, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15294028
Complete suboptimal folding of RNA and the stability of secondary structures.
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264
PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures.
Byun Y, Han K., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845039
Byun Y, Han K., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845039
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
Zuker M, Stiegler P., Nucleic Acids Res. 9(1), 1981
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Zuker M, Stiegler P., Nucleic Acids Res. 9(1), 1981
PMID: 6163133
RNA movies: visualizing RNA secondary structure spaces.
Evers D, Giegerich R., Bioinformatics 15(1), 1999
PMID: 10068690
Evers D, Giegerich R., Bioinformatics 15(1), 1999
PMID: 10068690
A three-stemmed mRNA pseudoknot in the SARS coronavirus frameshift signal.
Plant EP, Perez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Hennig M, Dinman JD., PLoS Biol. 3(6), 2005
PMID: 15884978
Plant EP, Perez-Alvarado GC, Jacobs JL, Mukhopadhyay B, Hennig M, Dinman JD., PLoS Biol. 3(6), 2005
PMID: 15884978
RNA pseudoknot prediction in energy based models
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Lyngsø RB, Pedersen CNS., 2001
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