publication . Article . Other literature type . 2014

The RNA shapes studio

Robert Giegerich; Stefan Janssen;
Open Access English
  • Published: 01 Oct 2014 Journal: Bioinformatics, volume 31, issue 3, pages 423-425 (issn: 1367-4803, eissn: 1367-4811, Copyright policy)
  • Publisher: Oxford University Press
  • Country: Germany
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 ...
Subjects
free text keywords: Applications Notes, Sequence Analysis, Bioinformatics, Nucleic acid structure, Minimal free energy, RNA, Manifold, Shape analysis (digital geometry), RNA Sequence, Theoretical computer science, Biology
Related Organizations
19 references, page 1 of 2

Baranov, PV. Programmed ribosomal frameshifting in decoding the sars-cov genome. Virology. 2005; 332: 498-510 [OpenAIRE] [PubMed]

Bernhart, S. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008; 9: 474 [OpenAIRE] [PubMed]

Burge, SW. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res.. 2013; 41: D226-D232 [OpenAIRE] [PubMed]

Darty, K. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics. 2009; 25: 1974-1975 [OpenAIRE] [PubMed]

Giegerich, R. A discipline of dynamic programming over sequence data. Sci. Comput. Program.. 2004a; 51: 215-263 [OpenAIRE]

Giegerich, R. Abstract shapes of RNA. Nucleic Acids Res.. 2004b; 32: 4843-4851 [OpenAIRE] [PubMed]

Janssen, S. Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics. 2011; 12: 429 [OpenAIRE] [PubMed]

Lorenz, R. ViennaRNA package 2.0. Algorithms Mol. Biol.. 2011; 6: 26 [OpenAIRE] [PubMed]

Lu, ZJ. Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA. 2009; 15: 1805-1813 [OpenAIRE] [PubMed]

Reeder, J, Giegerich, R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics. 2004; 5: 104 [OpenAIRE] [PubMed]

Reeder, J, Giegerich, R. Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics. 2005; 21: 3516-3523 [OpenAIRE] [PubMed]

Reeder, J. Locomotif: from graphical motif description to RNA motif search. Bioinformatics. 2007; 23: i392 [OpenAIRE] [PubMed]

Reinkensmeier, J. Conservation and occurrence of trans-encoded sRNAs in the rhizobiales. Genes. 2011; 2: 925-956 [OpenAIRE] [PubMed]

Sauthoff, G. Bellman’s GAP - a language and compiler for dynamic programming in sequence analysis. Bioinformatics. 2013; 29: 551-556 [OpenAIRE] [PubMed]

Steffen, P, Giegerich, R. Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics. 2005; 6: 224 [OpenAIRE] [PubMed]

19 references, page 1 of 2
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 ...
Subjects
free text keywords: Applications Notes, Sequence Analysis, Bioinformatics, Nucleic acid structure, Minimal free energy, RNA, Manifold, Shape analysis (digital geometry), RNA Sequence, Theoretical computer science, Biology
Related Organizations
19 references, page 1 of 2

Baranov, PV. Programmed ribosomal frameshifting in decoding the sars-cov genome. Virology. 2005; 332: 498-510 [OpenAIRE] [PubMed]

Bernhart, S. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008; 9: 474 [OpenAIRE] [PubMed]

Burge, SW. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res.. 2013; 41: D226-D232 [OpenAIRE] [PubMed]

Darty, K. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics. 2009; 25: 1974-1975 [OpenAIRE] [PubMed]

Giegerich, R. A discipline of dynamic programming over sequence data. Sci. Comput. Program.. 2004a; 51: 215-263 [OpenAIRE]

Giegerich, R. Abstract shapes of RNA. Nucleic Acids Res.. 2004b; 32: 4843-4851 [OpenAIRE] [PubMed]

Janssen, S. Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics. 2011; 12: 429 [OpenAIRE] [PubMed]

Lorenz, R. ViennaRNA package 2.0. Algorithms Mol. Biol.. 2011; 6: 26 [OpenAIRE] [PubMed]

Lu, ZJ. Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA. 2009; 15: 1805-1813 [OpenAIRE] [PubMed]

Reeder, J, Giegerich, R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics. 2004; 5: 104 [OpenAIRE] [PubMed]

Reeder, J, Giegerich, R. Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction. Bioinformatics. 2005; 21: 3516-3523 [OpenAIRE] [PubMed]

Reeder, J. Locomotif: from graphical motif description to RNA motif search. Bioinformatics. 2007; 23: i392 [OpenAIRE] [PubMed]

Reinkensmeier, J. Conservation and occurrence of trans-encoded sRNAs in the rhizobiales. Genes. 2011; 2: 925-956 [OpenAIRE] [PubMed]

Sauthoff, G. Bellman’s GAP - a language and compiler for dynamic programming in sequence analysis. Bioinformatics. 2013; 29: 551-556 [OpenAIRE] [PubMed]

Steffen, P, Giegerich, R. Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics. 2005; 6: 224 [OpenAIRE] [PubMed]

19 references, page 1 of 2
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