Active Motif

SeqCruncher™ Accelerator Announced

The SeqCruncher™ hardware accelerator delivers the performance of 550 CPU cores for next-generation TimeLogic® biocomputing systems

Redesigned FPGA accelerator outperforms prior model by 3-20X

Carlsbad, CA – March 27, 2008

Active Motif has introduced the SeqCruncher™ accelerator for the TimeLogic® biocomputing solutions. Designed to handle the explosion of data from next-generation sequencing endeavors, the SeqCruncher utilizes larger Xilinx® Field Programmable Gate Array (FPGA) chips and a faster PCIe interface to improve the processing of BLAST, Smith-Waterman, GeneDetective™ and Hidden Markov Model searches.

"Many genomics and genetics research teams have access to low-cost sequencing systems, but computing limitations can stall their data analysis," explained Joe Fernandez, CEO of Active Motif, Inc. "With SeqCruncher’s 3 to 20-fold speed improvements, our updated DeCypher® and CodeQuest™ systems will help researchers achieve the full potential of their sequencing programs," he continued.

"Oligo-length sequences are very important in genomics today, both for core facilities and biotech services," commented Christopher Hoover, TimeLogic® Marketing Manager. "The SeqCruncher architecture speeds high-sensitivity Smith-Waterman searches for shorter sequences by up to 15-fold. Mapping millions of short sequences (small RNAs, SNPs, short sequence reads, or microarray probes) to a genome with high sensitivity is now faster and significantly more cost-effective," Hoover continued.

For metagenomics research, categorizing millions of novel sequences using known protein families is a rigorous task. The SeqCruncher speeds the Hidden Markov Model (HMM) comparisons used for these studies. Compared to HMMer software running on a 2.66 Ghz Xeon CPU core, each SeqCruncher can deliver 550X more performance.

Ted DeFrank, President of Active Motif, remarked, "We are excited by the value the SeqCruncher products can bring to sequencing cores and smaller labs, and look forward to using our FPGA platform to accelerate additional next-generation genomic analyses.”

Interested parties may contact the TimeLogic® group for in-depth benchmark reports and custom tests on their critical sequence comparisons.