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                                    Bielefeld         University Bioinformatic Service
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Primer Design
RNA Studio
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RNA Studio

  • GUUGle GUUGle

    A utility for fast exact matching under RNA base pairing rules

  • InSilicoDicer Prediction of mature miRNA.

    Intrinsic and Extrinsic Prediction of mature miRNA.

  • 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.

  • pKiss

    pKiss is a tool for secondary structure prediction including kissing hairpin motifs.

  • pknotsRG RNA folding and thermodynamic matching

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

  • planACstar Implementation of Plan AC*

    planACstar is an implementation of plan AC* that improves structural RNA alignments by structure comparison

  • 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.

  • RNAforester2

    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.

Tue Jan 15 15:52:37 2013