Local Gapped Subforest Alignment and Its Application in Finding RNA Structural Motifs

RNA molecules whose secondary structures contain similar substructures often have similar functions. Therefore, an important task in the study of RNA is to develop methods for discovering substructures in RNA secondary structures that occur frequently (also referred to as motifs). In this paper, we consider the problem of computing an optimal local alignment of two given labeled ordered forests F1 and F2. This problem asks for a substructure of F1 and a substructure of F2 that exhibit a high similarity. Since an RNA molecule’s secondary structure can be represented as a labeled ordered forest, the problem we study has a direct application to finding potential motifs. We generalize the previously studied concept of a closed subforest to a gapped subforest and present the first algorithm for computing the optimal local gapped subforest alignment of F1 and F2. We also show that our technique can improve the time and space complexity of the previously most efficient algorithm for optim...

• Type: Conference
• Year: 2004
• Where: ISAAC
• Authors: Jesper Jansson, Ngo Trung Hieu, Wing-Kin Sung
• Keywords: Gapped Subforest, Gapped Subforest Alignment, ISAAC 2004, Secondary Structure