Journal
BIOINFORMATICS
Volume 22, Issue 4, Pages 500-503Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btk010
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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.
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