Vienna RNA web servers http://rna.tbi.univie.ac.at/

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Vienna RNA web servers http://rna.tbi.univie.ac.at/

RNA secondary structures The sequence of nucleotides of an RNA molecule carries the information required for its actual conformation in three dimensions. Zuker & Stiegler Nucleic Acids Res. 1981 Jan 10;9(1):133-48

Algorithms for structure prediction The partition function algorithm which calculates base pair probabilities based on the thermodynamic ranges – RNAfold The minimum free energy algorithm which yields a single optimal structure – RNAeval The suboptimal folding algorithm which generates all suboptimal structures within a given energy range of the optimal energy - RNAsubopt

RNAfold

Graphical representations

RNAalifold Predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. Limits of 3000 nts and 300 sequences in alignment.

LocARNA Produce pairwise and multiple structural alignments of RNA sequences.

RNAinverse Allows the design of RNA sequences for any desired target secondary structure. .....((((...))))...... NNNNNANNNNNNNNNUNNNNNN

RNAcofold Predict hybrid structure of two sequences

RNAz Detect thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. Unlike RNAlifold it predicts local secondary structures within alignments. No 3000 nt limit to number of nucleotides.

Results

RNAxs Design potent siRNAs to knock down your gene(s) of interest.

RNAup Predict RNA-RNA interactions and the accessibility of a target region.