RDfolder: a web server for prediction of RNA secondary structure

Prediction of RNA secondary structure is important in the functional analysis of RNA molecules. The RDfolder web server described in this paper provides two methods for prediction of RNA secondary structure: random stacking of helical regions and helical regions distribution. The random stacking method predicts secondary structure by Monte Carlo simulations. The method of helical regions distribution predicts secondary structure based on the helices that appear most frequently in the set of structures, which are generated by the random stacking method. The RDfolder web server can be accessed at http://rna.cbi.pku.edu.cn.

[1]  D. Turner,et al.  Predicting optimal and suboptimal secondary structure for RNA. , 1990, Methods in enzymology.

[2]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[3]  Li Wuju,et al.  Prediction of RNA secondary structure based on helical regions distribution , 1998, Bioinform..

[4]  C. E. Longfellow,et al.  Improved parameters for prediction of RNA structure. , 1987, Cold Spring Harbor symposia on quantitative biology.

[5]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[6]  Bjarne Knudsen,et al.  Pfold: RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars , 2003 .

[7]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[8]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[9]  Jan Krüger,et al.  RNA-related tools on the Bielefeld Bioinformatics Server , 2003, Nucleic Acids Res..

[10]  Pla Military,et al.  Computer aided design in high expression of recombinant ricin A chain in E.coli , 1998 .

[11]  L. W. Ju,et al.  GeneDn: for high-level expression design of heterologous genes in a prokaryotic system , 1998, Bioinform..

[12]  P. Higgs.  RNA secondary structure: physical and computational aspects , 2000, Quarterly Reviews of Biophysics.

[13]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[14]  D. Turner,et al.  Improved predictions of secondary structures for RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Pei Wu,et al.  The Gene Cloning and Bioactivity of the Expression Product of the Human FKBP12 , 2000 .