RNA Studio

• GUUGle GUUGle

  A utility for fast exact matching under RNA base pairing rules

• KnotInFrame Prediction of -1 ribosomal frameshifts

  KnotInFrame is a tool for predicting -1 ribosomal frameshifts with simple recursive pseudoknots as stimulating structural motif in mRNAs by means of the tool pknotsRG for the folding of the pseudoknots.

• Locomotif Localization of RNA motifs with generated thermodynamic Matchers

  A graphical programming system for RNA motif search.

• paRNAss Prediction of Alternate RNA Secondary Structures

  paRNAss is a software tool aiming to predict conformational switching in RNA.

• pknotsRG RNA folding and thermodynamic matching

  pknotsRG is a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots.

• RapidShapes RapidShapes

  RapidShapes computes the shapes above a specified probability threshold T by generating a list of promising shapes and constructing specialized folding programs for each shape to compute its probability. This aims at a heuristic improvement of runtime, while still computing exact probability values.

• RNA Movies

  RNA Movies is a system for the visualization of RNA secondary structure landscapes. Its input is a script consisting of structures from which animated graphical structure representations are generated. In this way, it creates the impression of an RNA-molecule moving through its own 2D structure space.

• RNAcast RNA consensus abstract shapes technique

  RNAcast (RNA consensus abstract shapes technique) is an alternative to the Sankoff algorithm for multiple RNA folding.

• RNAfold calculate secondary structures of RNAs

  RNA folding tool of the vienna RNA package.

• RNAforester

  RNA Forester is an alignment tool for RNA secondary structures. It is suitable for global comparision of RNA secondary structures and for finding similar regions between them.

• RNAhybrid

  RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA.

• RNAshapes

  RNAshapes offers three RNA analysis tools in one single software package: computation of a small set of representative structures of different shapes, computation of shape probabilities, and comparative prediction of consensus structures.

• RNAsifter RNA Shape Index Filter

  Searching and classifying non-coding RNAs with Rfam covariance models is currently considered ideal, but slow. RNAsifter is a structure-based filtering technique employing a pre-computed index of structural abstractions called shapes. Since RNAs are characterized by structure more than by sequence, our method is more sensible than sequence-based filters.