Full-text indexes provide fast substring search over large text collections. A serious problem
of these indexes has traditionally been their space consumption. A recent trend is to develop …

In 1990, Manber and Myers proposed suffix arrays as a space-saving alternative to suffix
trees and described the first algorithms for suffix array construction and use. Since that time …

The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at
varying evolutionary distances, as demonstrated by applications to multiple genomes. Two …

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 …

We describe a suffix-tree algorithm that can align the entire genome sequences of
eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The …

A new system for aligning whole genome sequences is described. Using an efficient data
structure called a suffix tree, the system is able to rapidly align sequences containing …

The MUMmer sequence alignment package is a suite of computer programs designed to
detect regions of homology in long biological sequences. Version 2.1 makes several …

We design two compressed data structures for the full-text indexing problem that support
efficient substring searches using roughly the space required for storing the text in …

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 …

The proliferation of online text, such as on the World Wide Web and in databases, motivates
the need for space-efficient index methods that support fast search. Consider a text T of n …