Algorithms for local similarity between forests

摘要

Anordered labelled tree is a tree where the left-to-right order among siblings is significant. Ordered labelled forests are sequences of ordered labelled trees. Given two ordered labelled forests F and G, the local forest similarity is to find two subforests F' and G' of F and G respectively such that they are the most similar over all possible F' and G'. In this paper, we present efficient algorithms for the local forest similarity problem for two types of sub-forests: sibling subforests and closed subforests.Our algorithms can be used to locate the structurally similar regions inRNA secondary structures since RNAmolecules' secondary structures could be represented as ordered labelled forests.