Efficient chaining of seeds in ordered trees

TL;DR

This paper introduces an efficient algorithm for chaining seeds in ordered trees, extending sequence chaining techniques to trees with applications in computational biology, especially RNA structure analysis.

Contribution

It presents a novel algorithm with improved complexity for chaining seeds in ordered trees, a problem relevant to biological data analysis.

Findings

Algorithm runs in O(m^2 log m) time and O(m^2) space.

Applicable to RNA secondary structure mining.

Extends sequence chaining methods to tree structures.

Abstract

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space.