RNAshapes: an integrated RNA analysis package based on abstract shapes. Steffen, P., Voß, B., Rehmsmeier, M., Reeder, J., & Giegerich, R. Bioinformatics, 22(4):500–503, February, 2006. 00193 bibtex*:Steffen:2006
RNAshapes: an integrated RNA analysis package based on abstract shapes [link]Paper  doi  abstract   bibtex   
Summary: 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. Availability: RNAshapes is freely available at http://bibiserv.techfak.uni-bielefeld.de/rnashapes/ as C source code, and as compiled binaries for the most common computer architectures. For Microsoft Windows, we also offer a graphical user interface with convenient access to the complete functionality of the package. Contact: psteffen@techfak.uni-bielefeld.de
@article{steffen_rnashapes:_2006,
	title = {{RNAshapes}: an integrated {RNA} analysis package based on abstract shapes},
	volume = {22},
	shorttitle = {{RNAshapes}},
	url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/4/500},
	doi = {10.1093/bioinformatics/btk010},
	abstract = {Summary: 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. Availability: RNAshapes is freely available at http://bibiserv.techfak.uni-bielefeld.de/rnashapes/ as C source code, and as compiled binaries for the most common computer architectures. For Microsoft Windows, we also offer a graphical user interface with convenient access to the complete functionality of the package. Contact: psteffen@techfak.uni-bielefeld.de},
	number = {4},
	urldate = {2009-03-10},
	journal = {Bioinformatics},
	author = {Steffen, Peter and Voß, Bjoern and Rehmsmeier, Marc and Reeder, Jens and Giegerich, Robert},
	month = feb,
	year = {2006},
	note = {00193
bibtex*:Steffen:2006},
	pages = {500--503}
}
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