RDfolder: A web server for prediction of RNA secondary structure

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Ying, Xiaomin ^b   Luo, Hong ^a   Luo, Jingchu ^a   Li, Wuju ^b  

^a PEKING UNIVERSITY   (China)

^b INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; RNA;

ACCESS TO INFORMATION; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; INTERNET; MONTE CARLO METHOD; NUCLEOTIDE SEQUENCE; ONLINE SYSTEM; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; RNA ANALYSIS; RNA STRUCTURE;

INTERNET; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION; RNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 3242889921     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh445     Document Type: Article

References (17)

1. Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
2. Jaeger,J.A., Turner,D.H. and Zuker,M. (1989) Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA, 86, 7706-7710.
3. Jaeger,J.A., Turner,D.H. and Zuker,M. (1990) Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol., 183, 281-306.
4. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
5. Knudsen,B. and Hein,J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31, 3423-3428.
6. Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
7. Sczyrba,A., Kruger,J., Mersch,H., Kurtz,S. and Giegerich,R. (2003) RNA-related tools on the Bielefeld Bioinformatics Server. Nucleic Acids Res., 31, 3767-3770.
8. Li,W,J. and Wu,J.J. (1996) Prediction of RNA secondary structure based on random stacking of helical regions. Acta Biophys. Sinica, 12, 213-218.
9. L promoter. Chin. J. Viol., 6, 111-116.
10. Li,W.J., Lei,H.X., Pei,W.H. and Wu,J.J. (1998) GeneDn: for high-level expression design of heterologous genes in a prokaryotic system. Bioinformatics, 14, 884-885.
11. Pei,W.H., Shen,B.F. and Li,W.J. (1998) Computer-aided design in high-expression of recombinant ricin-A chain in E.Coli. J. Cell. Mol. Immunol., 14, 33-36.
12. Pei,W.H., Hu,M.R., Li,W.J. and Shen,B.F. (2000) The gene cloning and bioactivity of the expression product of the human FKBP12. Chin. J. Biochem. Mol. Biol., 16, 322-325.
13. Li,W.J. and Wu,J.J. (1998) Prediction of RNA secondary structure based on helical regions distribution. Bioinformatics, 14, 700-706.
14. Turner,D.H., Sugimoto,N., Jaeger,J,A., Longfellow,C.E., Freier,S.M. and Kierzek,R. (1987) Improved parameters for prediction of RNA structure. Cold Spring Harbor Symp. Quant. Biol., 52, 123-133.
15. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
16. Griffiths,J.S., Bateman,A., Marshall,M., Khanna,A. and Eddy,S.R. (2003) Rfam: an RNA family database. Nucleic Acids Res., 31, 439-441.
17. Higgs,P.G. (2000) RNA secondary structure: physical and computational aspects. Q. Rev. Biophys., 33, 199-253.