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.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
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.
Erscheinungsjahr
2006
Zeitschriftentitel
Bioinformatics
Band
22
Ausgabe
4
Seite(n)
500-503
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1600421

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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. https://doi.org/10.1093/bioinformatics/btk010
Steffen, Peter, Voss, Björn, Rehmsmeier, Marc, Reeder, Jens, and Giegerich, Robert. 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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Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J., Bioinformatics 21(9), 2005
PMID: 15657094

AUTHOR UNKNOWN, MONATSHEFTE F CHEMIE 125(), 1994

AUTHOR UNKNOWN, SIAM J APPL MATH 45(), 1985

Shapiro, Bioinformatics 4(3), 1988
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
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