D-ASSIRC: Distributed program for finding sequence similarities in genomes

Abstract

Motivation: Locating the regions of similarity in a genome requires the availability of appropriate tools such as 'Accelerated Search for Similar Regions in Chromosomes' (ASSIRC; Vincens et al., Bioinformatics, 14, 715-725, 1998). The aim of this paper is to present different strategies for improving this program by distributing the operations and data to multiple processing units and to assess the efficiency of the different implementations in terms of running time as a function of the number of processing units. Results: The new version D-ASSIRC is based on three alternative strategies of task sharing: (1) a distributed search using the splitting of studied sequences into large overlapping subsequences (strategy ASS); (2) two distributed searches for repeated exact motifs of fixed size either managed by a central processor (strategy AGD) or locally managed by numerous processors (strategy ALD). The result is that the strategy ASS is suitable for a large number of processing units (the time was divided by a factor of 12 when the number of processing units was increased from 1 to 16) wheras the strategy ALD is better for a small set of processors (typically for four or six). The different proposed strategies are efficient for various applications in genomic research, particularly for locating similarities of nucleic sequences in large genomes.