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RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application
2020
Genes
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
doi:10.3390/genes12010014
pmid:33374382
fatcat:4b6cma4lxreifhuwta3tc4at44