TY - GEN

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 - 2009

Y1 - 2009

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 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(m2n(1 + log n/m))time [2]. We present a new algorithm that solves the problem for d-crossing structures in O(d m 2 nlogn) 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.

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 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(m2n(1 + log n/m))time [2]. We present a new algorithm that solves the problem for d-crossing structures in O(d m 2 nlogn) 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.

KW - RNA

KW - Sequence structure alignment

KW - Simultaneous alignment and folding

UR - http://www.scopus.com/inward/record.url?scp=70350629169&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-02441-2_21

DO - 10.1007/978-3-642-02441-2_21

M3 - Conference contribution

AN - SCOPUS:70350629169

SN - 3642024408

SN - 9783642024405

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 236

EP - 248

BT - Combinatorial Pattern Matching - 20th Annual Symposium, CPM 2009, Proceedings

T2 - 20th Annual Symposium on Combinatorial Pattern Matching, CPM 2009

Y2 - 22 June 2009 through 24 June 2009

ER -