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.