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The ViennaRNA Web Services

This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI homepage.

Our Web Services

Thermodynamic Structure Prediction

...predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences.

...predicts minimum free energy structures and base pair probabilities from single RNAs using a guiding potential based on SHAPE reactivity probing data.

...predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment.

...provides a detailed thermodynamic description of a sequence/structure pair.

...allows you to predict the secondary structure of a dimer.

...allows you to predict the accessibility of a target region.

ncRNA Detection

...will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments.

...will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments.

...allows you to predict the reading direction of evolutionarily conserved RNA secondary structures.

Folding Kinetics

...allows you to get insights into RNA folding kinetics.

Sequence Design

...allows you to design RNA sequences for any desired target secondary structure.

...assists you in siRNA design.

Genome Wide Screening

...predicts putative targets for sRNA-mRNA interactions in bacteria.

...predicts bacterial Transcription Start Sites from dRNA-seq data.

Other Web Services

...interactively draw and download RNA secondary structures.

...generates structural alignments from a set of sequences. (In collaboration with the Bioinformatics Group Freiburg).

...compares RNA family covariance models.

Databases

A database for the detailed investigation of AU-rich elements.

Downloads

Get the Source Code for:

  • the Vienna RNA Package, our basic RNA secondary structure analysis software.
  • the ALIDOT package for finding conserved structure motifs (add-on)
  • the barriers program for analysis of RNA folding landscapes.