RNAshapes A runtime heuristic to speed up the computation of accumulated shape probabilities
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RNAshapes Ranking & Summary

RNAshapes Tags

Number Computation mathematical computation shape computation model RNA abstraction computation Computation Override accumulated savings Visualize Probabilities Probabilities Plotter symbolic computation R6RS computation Heuristic Method heuristic calculation Computation details scientific computation geometric computation algebra computation heuristic scanner heuristic Computation Services numerical computation radiation computation heuristic algorithm accurate computation Savings Heuristic Method Parallel Computation incremental cut computation computation environment distribute computation VAR computation RNA sequence p-value computation stated density computation shape abstraction RNA analysis mY estimators computation study probabilities Computation Framework

RNAshapes Description

RapidShapes was developed to be a runtime heuristic to speed up the computation of accumulated shape probabilities. RNA shape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space. RNAshapes offers three powerful RNA analysis tools in one single software package: - Computation of a small set of representative structures of different shapes, complete in a well-defined sense. - Computation of accumulated shape probabilities. - Comparative prediction of consensus structures, as an alternative to the over-expensive Sankoff Algorithm.

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