RNAshapes: an integrated RNA analysis package based on abstract shapes

Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R (2006)
Bioinformatics 22(4): 500-503.

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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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Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 2006;22(4):500-503.
Steffen, P., Voss, B., Rehmsmeier, M., Reeder, J., & Giegerich, R. (2006). RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22(4), 500-503.
Steffen, P., Voss, B., Rehmsmeier, M., Reeder, J., and Giegerich, R. (2006). RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics 22, 500-503.
Steffen, P., et al., 2006. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22(4), p 500-503.
P. Steffen, et al., “RNAshapes: an integrated RNA analysis package based on abstract shapes”, Bioinformatics, vol. 22, 2006, pp. 500-503.
Steffen, P., Voss, B., Rehmsmeier, M., Reeder, J., Giegerich, R.: RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics. 22, 500-503 (2006).
Steffen, Peter, Voss, Björn, Rehmsmeier, Marc, Reeder, Jens, and Giegerich, Robert. “RNAshapes: an integrated RNA analysis package based on abstract shapes”. Bioinformatics 22.4 (2006): 500-503.
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11 References

Data provided by Europe PubMed Central.

A statistical sampling algorithm for RNA secondary structure prediction.
Ding Y, Lawrence CE., Nucleic Acids Res. 31(24), 2003
PMID: 14654704
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
An algorithm for comparing multiple RNA secondary structures
Shapiro, Bioinformatics 4(3), 1988
A comprehensive comparison of comparative RNA structure prediction approaches.
Gardner PP, Giegerich R., BMC Bioinformatics 5(), 2004
PMID: 15458580
Complete suboptimal folding of RNA and the stability of secondary structures.
Wuchty S, Fontana W, Hofacker IL, Schuster P., Biopolymers 49(2), 1999
PMID: 10070264
Fast folding and comparison of RNA secondary structures
Hofacker, Monatshefte für Chemie Chemical Monthly 125(2), 1994
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.
Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J., Bioinformatics 21(9), 2005
PMID: 15657094
Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems
Sankoff, SIAM Journal on Applied Mathematics 45(5), 1985

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