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.

Download
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
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
Zeitschriftentitel
NUCLEIC ACIDS RESEARCH
Band
35
Zeitschriftennummer
Web Server
Seite
W320-W324
ISSN
eISSN
PUB-ID

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. doi:10.1093/nar/gkm258
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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
1970-01-01T00:00:00Z

60 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

NS1' of flaviviruses in the Japanese encephalitis virus serogroup is a product of ribosomal frameshifting and plays a role in viral neuroinvasiveness.
Melian EB, Hinzman E, Nagasaki T, Firth AE, Wills NM, Nouwens AS, Blitvich BJ, Leung J, Funk A, Atkins JF, Hall R, Khromykh AA., J Virol 84(3), 2010
PMID: 19906906
Tfold: efficient in silico prediction of non-coding RNA secondary structures.
Engelen S, Tahi F., Nucleic Acids Res 38(7), 2010
PMID: 20047957
Stem-loop structure of Cocksfoot mottle virus RNA is indispensable for programmed -1 ribosomal frameshifting.
Tamm T, Suurväli J, Lucchesi J, Olspert A, Truve E., Virus Res 146(1-2), 2009
PMID: 19748532
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.
Popenda M, Blazewicz M, Szachniuk M, Adamiak RW., Nucleic Acids Res 36(database issue), 2008
PMID: 17921499
Shape based indexing for faster search of RNA family databases.
Janssen S, Reeder J, Giegerich R., BMC Bioinformatics 9(), 2008
PMID: 18312625
KnotInFrame: prediction of -1 ribosomal frameshift events.
Theis C, Reeder J, Giegerich R., Nucleic Acids Res 36(18), 2008
PMID: 18820303

14 References

Daten bereitgestellt von Europe PubMed Central.

Crystal structure of a hepatitis delta virus ribozyme.
Ferre-D'Amare AR, Zhou K, Doudna JA., Nature 395(6702), 1998
PMID: 9783582
The chemical repertoire of natural ribozymes.
Doudna JA, Cech TR., Nature 418(6894), 2002
PMID: 12110898
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH., J. Mol. Biol. 288(5), 1999
PMID: 10329189
Fast folding and comparison of RNA secondary structures
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P., 1994
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
RNA movies: visualizing RNA secondary structure spaces.
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
RNA pseudoknot prediction in energy based models
Lyngsø RB, Pedersen CNS., 2001

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 17478505
PubMed | Europe PMC

Suchen in

Google Scholar