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RNAstructure is a user-friendy software package for RNA and DNA secondary structure prediction and analysis that runs on Microsoft Windows. RNAstructure includes a secondary structure prediction algorithm, a partition function algorithm for predicting base pairing probabilities Dynalign for finding a structure common to multiple sequences, efn2 for predicting the stability of a secondary strcuture, OligoWalk for predicting binding affinity to an RNA target, and OligoScreen for predicting the unimolecular and bimolecular self structure for a large number of sequences.
Dynalign source code is available for local compilation.
OligoWalk can be used for siRNA design. Source code is also downloadable for local compilation.
PARTS source code for local compilation. PARTS finds a secondary structure common to two sequences and uses a partition function to calculate probabilities for each base pair in common secondary structures.