Please use this identifier to cite or link to this item:
https://scholarbank.nus.edu.sg/handle/10635/39448
DC Field | Value | |
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dc.title | Local gapped subforest alignment and its application in finding RNA structural motifs | |
dc.contributor.author | Jansson, J. | |
dc.contributor.author | Hieu, N.T. | |
dc.contributor.author | Sung, W.-K. | |
dc.date.accessioned | 2013-07-04T07:41:50Z | |
dc.date.available | 2013-07-04T07:41:50Z | |
dc.date.issued | 2004 | |
dc.identifier.citation | Jansson, J.,Hieu, N.T.,Sung, W.-K. (2004). Local gapped subforest alignment and its application in finding RNA structural motifs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 3341 : 569-580. ScholarBank@NUS Repository. | |
dc.identifier.issn | 03029743 | |
dc.identifier.uri | http://scholarbank.nus.edu.sg/handle/10635/39448 | |
dc.description.abstract | We consider the problem of computing an optimal local alignment of two labeled ordered forests F1 and F2 where ni and di, for i ∈{1, 2}, denote the number of nodes in Fi and the degree of Fi, respectively; and its applications in finding RNA structural motifs. A previous result is the local closed subforest alignment problem, which can be solved in O(n1n2d1d 2(d1 + d2)) time and O(n1n 2d1d2) space. This paper generalizes the concept of a closed subforest to a gapped subforest and then presents an algorithm for computing the optimal local gapped subforest alignment of F 1 and F2 in O(n1n2d 1d2(d1 + d2)) time and O(n 1n2d1d2) space. We show that our technique can improve the computation of the optimal local closed subforest alignment in O(n1n2(d1 + d2) 2) time and O(n1n2(d1 + d 2)) space. Furthermore, we prove that a special case of our local gapped subforest alignment problem is equivalent to a problem known in the literature as the local sequence-structure alignment problem (lssa). The previously best algorithm for lssa uses O(n1 2n 2 2(n1 + n2)) time and O(n 1n2) space; here, we show how to modify our main algorithm to obtain an algorithm for lssa running in O(n1n2(d 1 + d2)2) time and O(n1n 2(d1 + d2)) space. © Springer-Verlag 2004. | |
dc.source | Scopus | |
dc.type | Article | |
dc.contributor.department | COMPUTER SCIENCE | |
dc.description.sourcetitle | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | |
dc.description.volume | 3341 | |
dc.description.page | 569-580 | |
dc.identifier.isiut | NOT_IN_WOS | |
Appears in Collections: | Staff Publications |
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