RRC ID 65219
Author Lorenz R, Stadler PF.
Title RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application.
Journal Genes (Basel)
Abstract 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.
Volume 12(1)
Published 2020-12-24
DOI 10.3390/genes12010014
PII genes12010014
PMID 33374382
PMC PMC7823788
MeSH Algorithms Animals Base Pairing / genetics* Caenorhabditis elegans / genetics Models, Molecular* Nucleic Acid Conformation* RNA / chemistry RNA / genetics* Sequence Analysis, RNA Software Thermodynamics
Resource
C.elegans