0000000000489942
AUTHOR
Fabio Garofalo
Lightweight LCP construction for very large collections of strings
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several applications, especially in biological contexts. Nowadays, the input data for many problems are big collections of strings, for instance the data coming from "next-generation" DNA sequencing (NGS) technologies. In this paper we present the first lightweight algorithm (called extLCP) for the simultaneous computation of the longest common prefix array and the Burrows-Wheeler transform of a very large collection of strings having any length. The computation is reali…
The colored longest common prefix array computed via sequential scans
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the computation of statistics of the sequences in the dataset. Such computations become impractical in internal memory when very large collections of long sequences are considered. In this paper, we present a new conceptual data structure, the colored longest common prefix array (cLCP), that allows to efficiently tackle several problems with an alignment-free approach. In fact, we show that such a data structure can be computed via sequential scans in semi-exter…