We propose a new method to build persistent suffix trees for indexing the genomic data. Our algorithm DiGeST (Disk-Based Genomic Suffix Tree) improves significantly over previous ...
Marina Barsky, Ulrike Stege, Alex Thomo, Chris Upt...
A suffix tree is a fundamental data structure for string searching algorithms. Unfortunately, when it comes to the use of suffix trees in real-life applications, the current metho...
Marina Barsky, Ulrike Stege, Alex Thomo, Chris Upt...
This paper considers enumeration of substring equivalence classes introduced by Blumer et al. [1]. They used the equivalence classes to define an index structure called compact dir...
The indexing technique commonly used for long strings, such as genomes, is the suffix tree, which is based on a vertical (intra-path) compaction of the underlying trie structure. ...
A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Example...