September 2007

Conference Paper

Accelerating Genome Sequencing 100X with FPGAs

By:
Storaasli, Olaf O; Strenski, Dave
Page Number:
1-2
Book Title:
Proceedings of the 2007 Reconfigurable Systems Summer Institute (on DVD)
Publication Date:
September 2007
Conference Name:
Reconfigurable Systems Summer Institute (RSSI) 2007, National Center for Supercomputer Applications (NCSA)
Conference Location:
Urbana, Illinois, United States of America
Conference Sponsor:
National Center for Supercomputer Applications (NCSA), OpenFPGA and Manchester University (UK)

Abstract

The performance of two Cray XD1 systems with Virtex-II Pro 50 and Virtex-4 LX160 FPGAs was evaluated using the FASTA computational biology program for human genome (DNA and protein) sequence comparisons. FPGA speedups of 50X (Virtex-II Pro 50) and 100X (Virtex-4 LX160) over a 2.2 GHz Opteron were obtained. FPGA coding issues for human genome data are described.