Published:
TimeLogic Achieves the Performance of 471 CPU-Cores for HMM Searches Using Single FPGA Accelerator
Active Motif's TimeLogic® division announced
that their SeqCruncher(TM) PCIe accelerator card enables a single server to
search hidden Markov model (HMM) databases with the equivalent performance
of 471 Xeon CPU-cores.
Search tests were run to compare the performance range, flexibility and
scalability of the new SeqCruncher field programmable gate array (FPGA)
hardware and improved DeCypherHMM software against the established standard
open-source software, HMMER from Dr. Sean Eddy (HHMI). SeqCruncher provided
471x, 863x, and 1151x faster performance per CPU core with 1, 2 and 3 cards
when searching an HMM database.
"With one SeqCruncher accelerator installed in a 2 CPU server, we were able
to compare 1,000 proteins from the JCVI Global Ocean Sampling Expedition to
the Washington University St. Louis Pfam-fs database in 44 seconds. Running
HMMER software on the same 8-CPU core server took 43 minutes. This
performance makes our system ideal for any laboratory engaged in
metagenomics or high-throughput protein annotation," commented Darryl Leon,
Ph.D., Product Manager, Informatics at Active Motif.
The SeqCruncher also supports BLAST, Smith-Waterman and gene-modeling tools
for bioinformatics, and Active Motif has begun exploring ways to apply this
TimeLogic technology to computing burdens relating to next-generation
sequencing.
A full report of the SeqCruncher HMM performance details is available
online at http://www.timelogic.com/fpga_performance.html
About Active Motif, Inc.
Active Motif, founded in 1999, offers research kits, assays and
TimeLogic® biocomputing systems to enable scientists to explore the
relationships between genes, proteins and metabolic pathways. Active Motif
is headquartered in Carlsbad, California, and has international offices in
Tokyo, Japan; Brussels, Belgium; and Regensburg, Germany. Press contact:
Darryl León, Ph.D. Product Manager, Informatics Active Motif, Inc. tel.
877-222-9543, email: leon@activemotif.com, web site:
http://www.activemotif.com.
Copyright © 2009, MarketWire
Copyright © 2009, NewsBlaze,
Daily NewsTags: ,Computers and Software:Hardware, PharmaceuticalsandBiotech:EquipmentandSupplies, PharmaceuticalsandBiotech:Biotech, ,CA,CARLSBAD, CA
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