Improved Filters for the Approximate Suffix-Prefix Overlap Problem

Gregory Kucherov (1, 2) , Dekel Tsur (1)

1 Department of Computer Science [Beer-Sheva]
2 LIGM - Laboratoire d'Informatique Gaspard-Monge

Computing suffix-prefix overlaps for a large collection of strings is a fundamental building block for the analysis of genomic next-generation sequencing data. The approximate suffix-prefix overlap problem is to find all pairs of strings from a given set such that a prefix of one string is similar to a suffix of the other. Välimäki et al. (Information and Com-putation, 2012) gave a solution to this problem based on suffix filters. In this work, we propose two improvements to the method of Välimäki et al. that reduce the running time of the computation.

Domaines: Algorithme et structure de données [cs.DS]

Gregory Kucherov, Dekel Tsur. Improved Filters for the Approximate Suffix-Prefix Overlap Problem. SPIRE 2014, Oct 2014, Ouro Preto, Brazil. pp.139-148, ⟨10.1007/978-3-319-11918-2_14⟩. ⟨hal-01086208⟩