The RNA shapes studio

Janssen S, Giegerich R (2014)
Bioinformatics.

Journal Article | Published | English

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Abstract
Motivation: Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach.Results: We have rebuilt the original RNAshapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNAshapes, RNAalishapes and pknotsRG, including its recent extension pKiss. As a spin-off, we obtain heretofore unavailable functionality: e. g. with pKiss, we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool pAliKiss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways.Availability and implementation: As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio.Contact: bibi-help@cebitec.uni-bielefeld.de
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Janssen S, Giegerich R. The RNA shapes studio. Bioinformatics. 2014.
Janssen, S., & Giegerich, R. (2014). The RNA shapes studio. Bioinformatics.
Janssen, S., and Giegerich, R. (2014). The RNA shapes studio. Bioinformatics.
Janssen, S., & Giegerich, R., 2014. The RNA shapes studio. Bioinformatics.
S. Janssen and R. Giegerich, “The RNA shapes studio”, Bioinformatics, 2014.
Janssen, S., Giegerich, R.: The RNA shapes studio. Bioinformatics. (2014).
Janssen, Stefan, and Giegerich, Robert. “The RNA shapes studio”. Bioinformatics (2014).
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8 Citations in Europe PMC

Data provided by Europe PubMed Central.

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PMID: 26581440
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Barik S, Kumar A, Sarkar Das S, Yadav S, Gautam V, Singh A, Singh S, Sarkar AK., Sci Rep 5(), 2015
PMID: 26459056
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19 References

Data provided by Europe PubMed Central.

Programmed ribosomal frameshifting in decoding the SARS-CoV genome.
Baranov PV, Henderson CM, Anderson CB, Gesteland RF, Atkins JF, Howard MT., Virology 332(2), 2005
PMID: 15680415
RNAalifold: improved consensus structure prediction for RNA alignments.
Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF., BMC Bioinformatics 9(), 2008
PMID: 19014431
Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A., Nucleic Acids Res. 41(Database issue), 2013
PMID: 23125362
VARNA: Interactive drawing and editing of the RNA secondary structure.
Darty K, Denise A, Ponty Y., Bioinformatics 25(15), 2009
PMID: 19398448
A discipline of dynamic programming over sequence data
Giegerich R., 2004
Abstract shapes of RNA.
Giegerich R, Voss B, Rehmsmeier M., Nucleic Acids Res. 32(16), 2004
PMID: 15371549
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.
Janssen S, Schudoma C, Steger G, Giegerich R., BMC Bioinformatics 12(), 2011
PMID: 22051375
ViennaRNA Package 2.0.
Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL., Algorithms Mol Biol 6(), 2011
PMID: 22115189
Locomotif: from graphical motif description to RNA motif search.
Reeder J, Reeder J, Giegerich R., Bioinformatics 23(13), 2007
PMID: 17646322
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schluter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.
Sauthoff G, Mohl M, Janssen S, Giegerich R., Bioinformatics 29(5), 2013
PMID: 23355290
Versatile and declarative dynamic programming using pair algebras.
Steffen P, Giegerich R., BMC Bioinformatics 6(), 2005
PMID: 16156887
KnotInFrame: prediction of -1 ribosomal frameshift events.
Theis C, Reeder J, Giegerich R., Nucleic Acids Res. 36(18), 2008
PMID: 18820303
Prediction of RNA secondary structure including kissing hairpin motifs
Theis C., 2010
Structural analysis of aligned RNAs.
Voss B., Nucleic Acids Res. 34(19), 2006
PMID: 17020924
Complete probabilistic analysis of RNA shapes.
Voss B, Giegerich R, Rehmsmeier M., BMC Biol. 4(), 2006
PMID: 16480488

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