Next Article in Journal
Non-Invasive Prenatal Testing: Current Perspectives and Future Challenges
Next Article in Special Issue
DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification
Previous Article in Journal
MYC DNA Methylation in Prostate Tumor Tissue is Associated with Gleason Score
Previous Article in Special Issue
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
 
 
Article

RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application

by 1,* and 1,2,3,4,5,*
1
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
2
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
3
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
4
Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá 111321, Colombia
5
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
*
Authors to whom correspondence should be addressed.
Genes 2021, 12(1), 14; https://doi.org/10.3390/genes12010014
Received: 24 November 2020 / Revised: 18 December 2020 / Accepted: 21 December 2020 / Published: 24 December 2020
(This article belongs to the Special Issue Algorithms and Workflows in RNA Bioinformatics)
The accuracy of RNA secondary structure prediction decreases with the span of a base pair, i.e., the number of nucleotides that it encloses. The dynamic programming algorithms for RNA folding can be easily specialized in order to consider only base pairs with a limited span L, reducing the memory requirements to O(nL), and further to O(n) by interleaving backtracking. However, the latter is an approximation that precludes the retrieval of the globally optimal structure. So far, the ViennaRNA package therefore does not provide a tool for computing optimal, span-restricted minimum energy structure. Here, we report on an efficient backtracking algorithm that reconstructs the globally optimal structure from the locally optimal fragments that are produced by the interleaved backtracking implemented in RNALfold. An implementation is integrated into the ViennaRNA package. The forward and the backtracking recursions of RNALfold are both easily constrained to structural components with a sufficiently negative z-scores. This provides a convenient method in order to identify hyper-stable structural elements. A screen of the C. elegans genome shows that such features are more abundant in real genomic sequences when compared to a di-nucleotide shuffled background model. View Full-Text
Keywords: RNA secondary structure prediction; scanning algorithm; hyper-stable RNA elements RNA secondary structure prediction; scanning algorithm; hyper-stable RNA elements
Show Figures

Figure 1

MDPI and ACS Style

Lorenz, R.; Stadler, P.F. RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application. Genes 2021, 12, 14. https://doi.org/10.3390/genes12010014

AMA Style

Lorenz R, Stadler PF. RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application. Genes. 2021; 12(1):14. https://doi.org/10.3390/genes12010014

Chicago/Turabian Style

Lorenz, Ronny, and Peter F. Stadler. 2021. "RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application" Genes 12, no. 1: 14. https://doi.org/10.3390/genes12010014

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop