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 -