RNAshapes

RNAshapes: an integrated RNA analysis package based on abstract shapes. We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.

Keywords for this software

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References in zbMATH (referenced in 7 articles )

Showing results 1 to 7 of 7.
Sorted by year (citations)

  1. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  2. Fusy, Éric; Clote, Peter: Combinatorics of locally optimal RNA secondary structures (2014)
  3. Clote, Peter: Introduction to special issue on RNA (2008)
  4. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  5. Ponty, Yann: Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy (2008)
  6. Zhao, Jizhen; Malmberg, Russell L.; Cai, Liming: Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition (2008)
  7. Steffen, Peter; Vo; Rehmsmeier, Marc; Reeder, Jens; Giegerich, Robert: Rnashapes: An integrated RNA analysis package based on abstract shapes (2006) ioport


Further publications can be found at: http://bibiserv.techfak.uni-bielefeld.de/rnashapes/references.html