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Fast RNA structure alignment for crossing input structures. (English) Zbl 1216.68359
Summary: The complexity of pairwise RNA structure alignment depends on the structural restrictions assumed for both the input structures and the computed consensus structure. For arbitrarily crossing input and consensus structures, the problem is NP-hard. For non-crossing consensus structures, the algorithm of T. Jiang, G. Lin, B. Ma and K. Zhang [“A general edit distance between RNA structures”, J. Comput. Biol. 9, No. 2, 371–388 (2002)] computes the alignment in \(O(n^{2}m^{2})\) time where \(n\) and \(m\) denote the lengths of the two input sequences. If the input structures are also non-crossing, the problem corresponds to tree editing which can be solved in \(O(m^2n(1+\log \frac nm))\) time [E. D. Demaine et al., Lect. Notes Comput. Sci. 4596, 146–157 (2007; Zbl 1171.68843)]. We present a new algorithm that solves the problem for \(d\)-crossing structures in \(O(dm^2n \log n)\) time, where \(d\) is a parameter that is one for non-crossing structures, bounded by \(n\) for crossing structures, and much smaller than \(n\) on many practical examples. Crossing input structures allow for applications where the input is not a fixed structure but is given as base-pair probability matrices.
MSC:
68W40 Analysis of algorithms
68W32 Algorithms on strings
92D20 Protein sequences, DNA sequences
Software:
CONTRAfold
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