Algorithms to compute the Burrows-Wheeler Similarity Distribution

Autor(es)

Louza, Felipe A. ^[1] ; Telles, Guilherme P. ^[2] ; Gog, Simon ^[3] ; Zhao, Liang ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Dept Comp & Math, Ribeirao Preto - Brazil

^[2] Univ Estadual Campinas, Inst Comp, Campinas, SP - Brazil

^[3] eBay Inc, San Jose, CA - USA

• Tipo de documento: Artigo Científico
• Fonte: THEORETICAL COMPUTER SCIENCE; v. 782, p. 145-156, AUG 23 2019.
• Citações Web of Science: 1

Resumo

The Burrows-Wheeler transform (BWT) is a well studied text transformation widely used in data compression and text indexing. The BWT of two strings can also provide similarity measures between them, based on the observation that the more their symbols are intermixed in the transformation, the more the strings are similar. In this article we present two new algorithms to compute similarity measures based on the BWT for string collections. In particular, we present practical and theoretical improvements to the computation of the Burrows-Wheeler Similarity Distribution for all pairs of strings in a collection. Our algorithms take advantage of the BWT computed for the concatenation of all strings, and use compressed data structures that allow reducing the running time with a small memory footprint, as shown by a set of experiments with real and artificial datasets. (C) 2019 Elsevier B.V. All rights reserved. (AU)

• Processo FAPESP: 18/21509-2 - Transformada de Burrows-Wheeler e grafos de Bruijn sucintos
• Beneficiário: Felipe Alves da Louza
• Linha de fomento: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 17/09105-0 - Ordenação de sufixos e medidas de similaridade entre cadeias
• Beneficiário: Felipe Alves da Louza
• Linha de fomento: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 15/50122-0 - Fenômenos dinâmicos em redes complexas: fundamentos e aplicações
• Beneficiário: Elbert Einstein Nehrer Macau
• Linha de fomento: Auxílio à Pesquisa - Temático