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

fYear

2006

fDate

25-29 April 2006

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International

Conference_Location

Rhodes Island

Print_ISBN

1-4244-0054-6

Type

conf

DOI

10.1109/IPDPS.2006.1639532

Filename

1639532

Link To Document

https://search.isc.ac/dl/search/defaultta.aspx?DTC=49&DC=2048273