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Shapes Studio
The RNA shapes studio comprises four RNA secondary structure prediction tools, which make heavy use of shape abstraction.

An abstract shape is a mathematically well defined coarse grained view of an RNA structure, supporting the user to focus only on "interesting" structural features.

RNAshapes and pKiss operate on single sequence inputs. Their counterparts RNAalishapes and pAliKiss take an multiple sequence alignment as input. RNAshapes and RNAalishapes predict purely nested secondary structures. pKiss and pAliKiss additionally consider H-type pseudoknots and kissing hairpins.

KnotInFrame - KnotInFrame is a pipeline to predict ribosomal -1 frameshift sites with a simple pseudoknot as secondary structure in DNA and RNA sequences.

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

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

pknotsRG - RNA folding and thermodynamic matching

RapidShapes - Computes a thermodynamic matcher (TDM), using a runtime heuristic for probabilistic shape analysis.

RNAalishapes - R2222NA secondary structure prediction and shape abstraction for sequence alignments.

RNAshapes - RNA secondary structure prediction and shape abstraction for RNA sequences.