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RNAshapes logo    RNAshapes

Current version: RNAshapes 2.1.6 (Feb. 26. 2010)

Users and friends of RNAshapes. There is an updated version of RNAshapes available, which is based on Bellman's GAP. This version provides the same functionality within a modern web application. Consider using the latest version of RNAshapes for your task.

RNAshapes latest extension RapidShapes is now available online. RapidShapes is 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.

RNAshapes is available as C source code and compiled binaries for Unix, Mac OS X and Microsoft Windows. See download section.

RNAshapes can also be used online (submission section). This also links to a website that allows to study the combinatorics of shapes.

Users of RNAshapes at BiBiServ are requested to cite:
P. Steffen, B. Voß, M. Rehmsmeier, J. Reeder, and R. Giegerich.
RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22(4), 2006.
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Fri May 3 15:04:54 2013