SEARCHING FOR A FAMILY OF ORPHAN SEQUENCES WITH SAMBA, A PARALLEL HARDWARE DEDICATED TO BIOLOGICAL APPLICATIONS

A significant proportion of coding sequences or open reading frames di scovered in the course of sequencing projects do not show any similari ty with other sequences deposited with the protein databanks. In such cases the search for similarities must be performed with as many compa rison algorithms as possible, so as to increase the chance of finding weak relationships. A specialised parallel hardware (SAMBA) implementi ng the Smith & Waterman algorithm has been developed at the 'Institut de Recherche en Informatique et Systemes Aleatoires' (IRISA). It makes it possible to scan protein databanks at a speed comparable with that of BLAST or FASTA. We report here a study performed with SAMBA on 814 orphan sequences from S cerevisiae and compare the results with those from BLAST and FASTA.