Vienna RNA secondary structure server

The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently offers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences and the design of sequences that will fold into a predefined structure. All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/.

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

[2]  Robert E. Bruccoleri,et al.  An improved algorithm for nucleic acid secondary structure display , 1988, Comput. Appl. Biosci..

[3]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[4]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[5]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[6]  M. Zuker,et al.  "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. , 1995, Nucleic acids research.

[7]  Laurie J. Heyer,et al.  Finding the most significant common sequence and structure motifs in a set of RNA sequences. , 1997, Nucleic acids research.

[8]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[9]  M. Huynen,et al.  Automatic detection of conserved RNA structure elements in complete RNA virus genomes. , 1998, Nucleic acids research.

[10]  V. Juan,et al.  RNA secondary structure prediction based on free energy and phylogenetic analysis. , 1999, Journal of molecular biology.

[11]  Bjarne Knudsen,et al.  RNA secondary structure prediction using stochastic context-free grammars and evolutionary history , 1999, Bioinform..

[12]  R. Lück,et al.  ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure. , 1999, Nucleic acids research.

[13]  P. Schuster,et al.  Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.

[14]  James W. Brown,et al.  RNAML: a standard syntax for exchanging RNA information. , 2002, RNA.

[15]  P. Stadler,et al.  Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.