Title :
Some initial results on hardware BLAST acceleration with a reconfigurable architecture
Author :
Sotiriades, Euripides ; Kozanitis, Christos ; Dollas, Apostolos
Author_Institution :
Dept. of Electron. & Comput. Eng., Tech. Univ. of Crete
Abstract :
The BLAST algorithm is the prevalent tool that is used by molecular biologists for DNA sequence matching and database search. In this work we demonstrate that with an appropriate reconfigurable architecture, BLAST performance can be improved with a single-chip solution 5 times over a specialized and optimized computer cluster, or 37 times over a single computer. These initial results account for I/O and are very encouraging for the development of a large scale, reconfigurable BLAST engine
Keywords :
biocomputing; molecular biophysics; query processing; reconfigurable architectures; BLAST performance; DNA sequence matching; computer cluster; database search; molecular biology; reconfigurable architecture; single-chip solution; Acceleration; Biology computing; Clustering algorithms; DNA; Databases; Engines; Hardware; Large-scale systems; Reconfigurable architectures; Sequences;
Conference_Titel :
Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International
Conference_Location :
Rhodes Island
Print_ISBN :
1-4244-0054-6
DOI :
10.1109/IPDPS.2006.1639532
