Title :
Systolic filter for fast DNA similarity search
Author :
Guerdoux-Jamet, P. ; Lavenier, D.
Author_Institution :
IRISA, Rennes, France
Abstract :
This paper presents a systolic filter for speeding up the scan of DNA databases. The filter acts as a co-processor which performs the more intensive computations occurring during the process. Our validation, based on a FPGA prototype board tightly connected to a workstation, has shown that the filter may boost the performance of the machine by a factor ranging from 50 to 400 over current workstations
Keywords :
DNA; biology computing; coprocessors; digital filters; field programmable gate arrays; pattern matching; reconfigurable architectures; systolic arrays; DNA databases; FPGA prototype board; co-processor; fast DNA similarity search; systolic filter; Computational complexity; DNA; Databases; Field programmable gate arrays; Filters; Nuclear measurements; Prototypes; Sequences; Software performance; Workstations;
Conference_Titel :
Application Specific Array Processors, 1995. Proceedings. International Conference on
Conference_Location :
Strasbourg
Print_ISBN :
0-8186-7109-2
DOI :
10.1109/ASAP.1995.522918
