Fast RNA Structure Alignment for Crossing Input Structures

Authors:
Rolf Backofen;Gad M. Landau;Mathias Möhl;Dekel Tsur;Oren Weimann
Affiliations:
Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany;Department of Computer Science, Haifa University, Haifa 31905, Israel Department of Computer and Information Science, Polytechnic Institute of NYU, Six MetroTech Center, Brooklyn NY 11201-3840;Programming Systems Lab, Saarland University, Saarbrücken, Germany;Ben-Gurion University, Beer-Sheva, Israel;Massachusetts Institute of Technology, Cambridge, USA MA 02139
Venue:
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Year:
2009

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Abstract

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, Jiang et al's algorithm [1] computes the alignment in O (n 2 m 2) time where n and m denote the lengths of the two input sequences. If also the input structures are non-crossing, the problem corresponds to tree editing which can be solved in $O(m^2n(1+\log\frac{n}{m}))$ time [2]. We present a new algorithm that solves the problem for d -crossing structures in O (d m 2 n logn ) 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 most practical examples. Crossing input structures allow for applications where the input is not a fixed structure but is given as base-pair probability matrices.