Efficient chaining of seeds in ordered trees
Quantitative Methods
2015-05-19 v1
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.
Keywords
Cite
@article{arxiv.1007.0942,
title = {Efficient chaining of seeds in ordered trees},
author = {Julien Allali and Cédric Chauve and Pascal Ferraro and Anne-Laure Gaillard},
journal= {arXiv preprint arXiv:1007.0942},
year = {2015}
}