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Bioinformatics. 2006 Feb 15;22(4):500-3. Epub 2005 Dec 15.

RNAshapes: an integrated RNA analysis package based on abstract shapes.

Author information

1
Faculty of Technology and, Bielefeld University, 33594 Bielefeld, Germany. psteffen@techfak.uni-bielefeld.de

Abstract

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.

PMID:
16357029
DOI:
10.1093/bioinformatics/btk010
[Indexed for MEDLINE]

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