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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

RNAfold server

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

Goto Webserver »

RNAprobing server

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

Goto Webserver »

RNAalifold server

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

Goto Webserver »

RNAeval server

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

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RNAcofold server

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

Goto Webserver »

RNAup server

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

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ncRNA Detection

Structure conservation analysis server

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

Goto Webserver »

RNAz server

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

Goto Webserver »

RNAstrand server

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

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Bcheck

...predicts rnpB genes.

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Folding Kinetics

Barriers / Treekin Server

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

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Sequence Design

RNAinverse server

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

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RNAxs server

...assists you in siRNA design.

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Genome Wide Screening

RNApredator

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

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TSSAR

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

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Other Web Services

forna webserver

...interactively draw and download RNA secondary structures.

Goto Webserver »

LocARNA server

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

Goto Webserver »

CMCompare webserver

...compares RNA family models.

Goto Webserver »

Databases

AREsite

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

Browse Database »

Atlas of conserved Viral RNA Structures

A database of conserved RNA secondary structures for various virus families (predicted using ALIDOT).

Browse Database »

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.