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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 web server.

Web Servers

Thermodynamic Structure Prediction
  • RNAfold server...
    ...predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences.
  • RNAalifold server...
    ...predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment.
  • RNAeval server...
    ...provides a detailed thermodynamic description of a sequence/structure pair.
  • RNAcofold server...
    ...allows you to predict the secondary structure of a dimer.
  • RNAup server...
    ...allows you to predict the accessibility of a target region.
ncRNA Prediction
  • Structure conservation analysis server...
    ...will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments.
  • RNAz server...
    ...will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments.
  • Bcheck...
    ...predicts rnpB genes.
  • RNAstrand server...
    ...allows you to predict the reading direction of evolutionarily conserved RNA secondary structures.
Folding Kinetics
  • barriers server...
    ...allows you to get insights into RNA folding kinetics.
Sequence Design
  • RNAinverse server...
    ...allows you to design RNA sequences for any desired target secondary structure.
  • RNAxs server...
    ...assists you in siRNA design.
Genome Wide Screening
  • RNApredator...
    ...predicts targets of small bacterial RNAs
  • TSSAR...
    ...predicts bacterial Transcription Start Sites from dRNA-seq data.
Other Web Services

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.