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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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