A faster algorithm for simultaneous alignment and folding of RNA

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Michal Ziv-UkelsonRon Shamir

Abstract

The current pairwise RNA (secondary) structural alignment algorithms are based on Sankoff's dynamic programming algorithm from 1985. Sankoff's algorithm requires O(N(6)) time and O(N(4)) space, where N denotes the length of the compared sequences, and thus its applicability is very limited. The current literature offers many heuristics for speeding up Sankoff's alignment process, some making restrictive assumptions on the length or the shape of the RNA substructures. We show how to speed up Sankoff's algorithm in practice via non-heuristic methods, without compromising optimality. Our analysis shows that the expected time complexity of the new algorithm is O(N(4)sigma(N)), where sigma(N) converges to O(N), assuming a standard polymer folding model which was supported by experimental analysis. Hence, our algorithm speeds up Sankoff's algorithm by a linear factor on average. In simulations, our algorithm speeds up computation by a factor of 3-12 for sequences of length 25-250. Code and data sets are available, upon request.

References

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Citations

Oct 13, 2012·Bioinformatics·Kengo SatoYasubumi Sakakibara
Aug 20, 2011·Algorithms for Molecular Biology : AMB·Shay ZakovMichal Ziv-Ukelson
Jan 5, 2011·Algorithms for Molecular Biology : AMB·Mathias MöhlS Cenk Sahinalp
Aug 9, 2016·Algorithms for Molecular Biology : AMB·Yelena Frid, Dan Gusfield
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Slavica Dimitrieva, Philipp Bucher

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Software Mentioned

FoldalignM
ComputeBeam
RNAAlifold
FoldAlign SA
fastCoFold
FoldAlign
Dynalign
DeclareMathSizes
PMCOMP

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