A new algorithm for sparse suffix trees

Authors:
Gustavo Akio T. Sacomoto;Alair Pereira do Lago
Affiliations:
Université Lyon, CNRS, UMR, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France and INRIA Rhône-Alpes, Montbonnot Saint-Martin, France;Universidade de São Paulo, Instituto de Matemática e Estatística, São Paulo, Brazil
Venue:
BSB'11 Proceedings of the 6th Brazilian conference on Advances in bioinformatics and computational biology
Year:
2011

Citing 4
Cited 0

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Abstract

The sparse suffix trees are suffix trees in which some suffixes are omitted. There are many applications for these structures, ranging from bioinformatics to natural language processing. In many cases, they can replace the complete suffix tree, without decreasing the performance, but with expressive gains in memory consumption. Here, we present a new optimal algorithm to build the sparse suffix tree. That algorithm is simple enough to be implemented and to obtain good results in practice.