Searching for a family of orphan sequence with SAMBA,
a parallel hardware dedicated to biological applications

Pascale GUERDOUX-JAMET - Jean Loup RISLER


BIOCHIMIE, 78, 311-314, 1996

Abstract

A significant proportion of coding sequences or open reading frames dicovered in the course of sequencing projects do not show any similarity with other sequences deposited with the protein databanks. In such cases, the search for similarities must be performed with as many comparison algorithms as possible, so as to increase the chance of finding weak realtionships. A specialised parallel hardware (SAMBA) implementing the Smith and Waterman algorithm has been developed at IRISA. It makes it possible to scan protein databanks at a speed comparable with that of BLAST or FASTA. We report here a study performes with SAMBA on 814 orphan sequences from S. cerevisiae and compare the results with those from BLAST and FASTA.