TY - JOUR

T1 - Fast RNA structure alignment for crossing input structures

AU - Backofen, Rolf

AU - Landau, Gad M.

AU - Möhl, Mathias

AU - Tsur, Dekel

AU - Weimann, Oren

PY - 2011/3/1

Y1 - 2011/3/1

N2 - 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 (2002) [9] algorithm computes the alignment in O(n2m2) 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(m2n(1+lognm)) time (Demaine et al., 2007) [3]. We present a new algorithm that solves the problem for d-crossing structures in O(dm2nlogn) 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.

AB - 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 (2002) [9] algorithm computes the alignment in O(n2m2) 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(m2n(1+lognm)) time (Demaine et al., 2007) [3]. We present a new algorithm that solves the problem for d-crossing structures in O(dm2nlogn) 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.

KW - RNA

KW - Sequence structure alignment

KW - Simultaneous alignment and folding

UR - http://www.scopus.com/inward/record.url?scp=79551599587&partnerID=8YFLogxK

U2 - 10.1016/j.jda.2010.07.004

DO - 10.1016/j.jda.2010.07.004

M3 - Article

AN - SCOPUS:79551599587

VL - 9

SP - 2

EP - 11

JO - Journal of Discrete Algorithms

JF - Journal of Discrete Algorithms

SN - 1570-8667

IS - 1

ER -