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Bioinformatics Vol. 18 no. 3 2002
Pages 446-451
© 2002 Oxford University Press

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

Pierre Vincens 1,2,*, Anne Badel-Chagnon 2, Cécile André 3 and Serge Hazout 2

1 Département de Biologie (FR 36), Ecole Normale Supérieure, 46 rue d’Ulm, 75230 Paris Cedex 05, France
2 Equipe de Bioinformatique Génomique et Moléculaire, INSERM U436, UniversitéParis 7, case 7113, 2 Place Jussieu, 75251 Paris Cedex 05, France
3 Département de Biomathématiques, CHU Pitié-Salpétrière, 91 boulevard de l’Hôpital, 75634 Paris Cedex 13, France

Received on April 4, 2001 ; revised on July 26, 2001 ; accepted on September 19, 2001

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-ASSIRCis 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 ASSis 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 ALDis 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.

Availability: D-ASSIRCis freely available by anonymous FTP at ftp://ftp.ens.fr/pub/molbio/dassirc.tar.gz. Sources and binaries for Solaris and Linux are included in the distribution.

Contact: vincens{at}biologie.ens.fr

* To whom correspondence should be addressed.


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