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GUUGle GUUGle
A utility for fast exact matching under RNA base pairing
rules
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InSilicoDicer
Prediction of mature miRNA.
Intrinsic and Extrinsic Prediction of mature miRNA.
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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.
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Locomotif
Localization of RNA motifs with generated thermodynamic
Matchers
A graphical programming system for RNA motif search.
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paRNAss Prediction of
Alternate RNA Secondary Structures
paRNAss is a software tool aiming to predict
conformational switching in RNA.
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pKiss
pKiss is a tool for secondary structure prediction
including kissing hairpin motifs.
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pknotsRG RNA folding
and thermodynamic matching
pknotsRG is a tool for folding RNA secondary structures,
including the class of simple recursive pseudoknots.
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planACstar
Implementation of Plan AC*
planACstar is an implementation of plan AC* that improves
structural RNA alignments by structure comparison
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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.
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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.
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RNAcast RNA consensus
abstract shapes technique
RNAcast (RNA consensus abstract shapes technique) is an
alternative to the Sankoff algorithm for multiple RNA
folding.
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RNAfold calculate
secondary structures of RNAs
RNA folding tool of the vienna RNA package.
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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.
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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.
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RNAhybrid
RNAhybrid is a tool for finding the minimum free energy
hybridisation of a long and a short RNA.
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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.
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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.