RNAshapes: an integrated RNA analysis package based on abstract shapes

@article{Steffen2006RNAshapesAI,
  title={RNAshapes: an integrated RNA analysis package based on abstract shapes},
  author={Peter Steffen and Bj{\"o}rn Vo\ss and Marc Rehmsmeier and Jens Reeder and Robert Giegerich},
  journal={Bioinformatics},
  year={2006},
  volume={22 4},
  pages={500-3}
}
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… CONTINUE READING
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