RIscoper (RNA Interactome Scoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model.
RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.
jViz.Rna is a multi-platform visualization tool capable of displaying and comparing RNA secondary structures encoded in a number of file formats. Structures can be shown using six different visualization modes including a numerical analysis mode which includes sensitivity and specificity. Any of the drawings and data produced can be saved in a variety of formats enabling easy usage in publications and presentations.
RNAHeliCes is a tool for RNA folding space analysis. It abstracts from structural detail and maps structures using a position-specific abstraction based on helices.
RCAS facilitates biological discovery from target regions located by methods such as Clip-Seq. RCAS automatically provides dynamic annotations for custom input files that contain transcriptomic target regions.