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An IP algorithm for RNA folding trajectories. (English) Zbl 1443.92135
Schwartz, Russell (ed.) et al., 17th international workshop on algorithms in bioinformatics, WABI 2017, Boston, MA, USA, August 21–23, 2017. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 88, Article 6, 16 p. (2017).
Summary: Vienna RNA package software Kinfold implements the Gillespie algorithm for RNA secondary structure folding kinetics, for the move sets $$MS_1$$ [resp. $$MS_2]$$, consisting of base pair additions and removals [resp. base pair addition, removals and shifts]. In this paper, for arbitrary secondary structures $$s,t$$ of a given RNA sequence, we present the first optimal algorithm to compute the shortest $$MS_2$$ folding trajectory $$s=s_0, s_1,\ldots,s_m=t$$, where each intermediate structure $$s_{i+1}$$ is obtained from its predecessor by the addition, removal or shift of a single base pair. The shortest $$MS_1$$ trajectory between $$s$$ and $$t$$ is trivially equal to the number of base pairs belonging to $$s$$ but not $$t$$, plus the number of base pairs belonging to $$t$$ but not $$s$$. Our optimal algorithm applies integer programming (IP) to solve (essentially) the minimum feedback vertex set (FVS) problem for the “conflict digraph” associated with input secondary structures $$s,t$$, and then applies topological sort, in order to generate an optimal $$MS_2$$ folding pathway from $$s$$ to $$t$$ that maximizes the use of shift moves. Since the optimal algorithm may require excessive run time, we also sketch a fast, near-optimal algorithm (details to appear elsewhere). Software for our algorithm will be publicly available at http://bioinformatics.bc.edu/clotelab/MS2distance/.
For the entire collection see [Zbl 1372.68022].
MSC:
 92D20 Protein sequences, DNA sequences 90C10 Integer programming 92-04 Software, source code, etc. for problems pertaining to biology
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