The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic
study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic …

The suffix tree is one of the most important data structures in string processing and comparative
genomics. However, the space consumption of the suffix tree is a bottleneck in large …

Term rewriting techniques are applicable to various fields of computer science, including
software engineering, programming languages, computer algebra, program verification, …

A team at the Lawrence Livermore National Laboratory (LLNL) was given the task of using
computational tools to speed up the development of DNA diagnostics for pathogen detection. …

Motivation: To allow a direct comparison of the genomic DNA sequences of sufficiently
similar organisms, there is an urgent need for software tools that can align more than two …

In large scale applications as computational genome analysis, the space requirement of the
suffix tree is a severe drawback. In this paper, we present a uniform framework that enables …

We introduce and study the problem of compressed indexed sequence of strings, ie representing
indexed sequences of strings in nearly-optimal compressed space, while preserving …

During evolution, genomes are subject to genome rearrangements that alter the ordering
and orientation of genes on the chromosomes. If a genome consists of a single chromosome (…

Motivation: Low-cost genome sequencing gives unprecedented complete information about
the genetic structure of populations, and a population graph captures the variations between …

Given n fragments from k>2 genomes, Myers and Miller showed how to find an optimal global
chain of colinear non-overlapping fragments in O(nlog k n) time and O(nlog k−1 n) space. …