Title :
Design Space Exploration for the BLAST Algorithm Implementation
Author :
Sotiriades, Euripides ; Dollas, Apostolos
Author_Institution :
Tech. Univ. of Crete, Chania
Abstract :
The most prevalent algorithm for DNA sequence matching is the BLAST algorithm. We have developed several FPGA-based architectures to speed up BLAST execution. In this work we present a new VLSI architecture as a followup to our reconfigurable logic-based architectures, and we compare the performance of several software and hardware implementations of BLAST.
Keywords :
DNA; VLSI; biology computing; logic design; molecular biophysics; reconfigurable architectures; BLAST algorithm implementation; DNA sequence matching; FPGA-based architecture; VLSI architecture; design space exploration; reconfigurable logic architecture; Algorithm design and analysis; Computer architecture; DNA computing; Databases; Field programmable gate arrays; Hardware; Parallel processing; Software algorithms; Space exploration; Very large scale integration;
Conference_Titel :
Field-Programmable Custom Computing Machines, 2007. FCCM 2007. 15th Annual IEEE Symposium on
Conference_Location :
Napa, CA
Print_ISBN :
978-0-7695-2940-0
DOI :
10.1109/FCCM.2007.36
