RNA sequences - Vienna RNA Package
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
RNA secondary structure prediction through energy minimization is the most used function in the package. Three kinds of dynamic programming algorithms for structure prediction are provided :
the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure,
the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble,
and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy.
For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, an algorithm to design sequences with a predefined structure (inverse folding) is provided.
RNAfold predicts minimum energy secondary structures and pair probabilities
RNAeval evaluates energy of RNA secondary structures
RNAheat calculates the specific heat (melting curve) of an RNA sequence
RNAinverse : inverse fold (design) sequences with predefined structure
RNAdistance compares secondary structures
RNApdist compares base pair probabilities
RNAsubopt : complete suboptimal folding
RNAplot : RNA structure drawings in PostScript, SVG, or GML
RNAcofold predicts hybrid structure of two sequences
RNAduplex predicts possible hybridization sites between two sequences
RNAalifold predicts the consensus structure of several aligned sequences
RNALfold predicts locally stable structure of long sequences
RNAplfold computes average pair probabilities for local base pairs in long sequences
RNApaln : fast structural alignment of RNA sequences using string alignments