Local gapped subforest alignment and its application in finding RNA structural motifs

  • Authors:

  • Jesper Jansson;Ngo Trung Hieu;Wing-Kin Sung

  • Affiliations:

  • School of Computing, National University of Singapore, Singapore;School of Computing, National University of Singapore, Singapore;School of Computing, National University of Singapore, Singapore

  • Venue:
  • ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
  • Year:
  • 2004

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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(n1n2d1d2 (d1+d2)) time and O(n1n2d1d2) 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 F1 and F2 in O(n1n2d1d2 (d1 + d2)) time and O(n1n2d1d2) 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 + d2)) 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(n12n22 (n1 + n2)) time and O(n1n2) space; here, we show how to modify our main algorithm to obtain an algorithm for lssa running inO(n1n2 (d1 + d2)2) time and O(n1n2 (d1 + d2)) space.