Bioinformatics Advance Access originally published online on December 15, 2005
Bioinformatics 2006 22(4):500-503; doi:10.1093/bioinformatics/btk010
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RNAshapes: an integrated RNA analysis package based on abstract shapes
1Faculty of Technology and, Bielefeld University 33594 Bielefeld, Germany
2Center for Biotechnology (Ce BiTec), Bielefeld University 33594 Bielefeld, Germany
3Institute of Biology II, Experimental Bioinformatics, Freiburg University Schänzlestr. 1, 79104 Freiburg, Germany
*To whom correspondence should be addressed.
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{at}techfak.uni-bielefeld.de
Received on October 25, 2005; revised on December 13, 2005; accepted on December 14, 2005
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Sczyrba, S. Konermann, and R. Giegerich Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server Brief Bioinform, May 1, 2008; 9(3): 243 - 249. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. C. Lynn, P. Skewes-Cox, Y. Kosaka, M. T. McManus, B. D. Harfe, and M. S. German MicroRNA Expression Is Required for Pancreatic Islet Cell Genesis in the Mouse Diabetes, December 1, 2007; 56(12): 2938 - 2945. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Freyhult, V. Moulton, and P. Clote Boltzmann probability of RNA structural neighbors and riboswitch detection Bioinformatics, August 15, 2007; 23(16): 2054 - 2062. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Xu, Y. Ji, and G. D. Stormo RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment Bioinformatics, August 1, 2007; 23(15): 1883 - 1891. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Freyhult, V. Moulton, and P. Clote RNAbor: a web server for RNA structural neighbors Nucleic Acids Res., July 13, 2007; 35(suppl_2): W305 - W309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kaiser, J. Kruger, and D. J. Evers RNA Movies 2: sequential animation of RNA secondary structures Nucleic Acids Res., July 13, 2007; 35(suppl_2): W330 - W334. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Ritchie, M. Legendre, and D. Gautheret RNA stem-loops: To be or not to be cleaved by RNAse III RNA, April 1, 2007; 13(4): 457 - 462. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Kim, H. H. Gan, and T. Schlick A computational proposal for designing structured RNA pools for in vitro selection of RNAs RNA, April 1, 2007; 13(4): 478 - 492. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Voss Structural analysis of aligned RNAs Nucleic Acids Res., November 14, 2006; 34(19): 5471 - 5481. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Berezikov, G. van Tetering, M. Verheul, J. van de Belt, L. van Laake, J. Vos, R. Verloop, M. van de Wetering, V. Guryev, S. Takada, et al. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis Genome Res., October 1, 2006; 16(10): 1289 - 1298. [Abstract] [Full Text] [PDF]
|
|