TimeLogic Corporation Releases New BLAST With Over 1,200X Speed-Up

Published: Apr 02, 2013

Carlsbad, CA—April 1, 2013 -- TimeLogic, a division of Active Motif, has released an update to their popular FPGA-accelerated BLAST implementation, Tera-BLAST, which is now capable of delivering over 1,200x speed-up as compared to software-only versions. “This version of Tera-BLAST, which runs on our J-Series Field Programmable Gate Array (FPGA) Similarity Search Engine, allows us to replace a cluster of dozens of high performance servers with a single DeCypher system,” commented Michael Murray, Manager of Sales & Marketing activities for TimeLogic products at Active Motif. Furthermore, “assembling multi-node DeCypher systems is a simple affair and TimeLogic already has the requisite system administration, job queuing and job distribution functionality built-into our DeCypher software, making it easy for our customers to replace a full rack of powerful servers with a small DeCypher system.”

Engineering Manager at TimeLogic, Steve Stelman, added “Our new Tera-BLAST whitepaper details the over 1,200x acceleration we achieve as compared to NCBI BLAST running on a Xeon E5-2690 2.90GHz core. Our benchmark tests were run with 1.2 mega-symbols of query proteins (3,266 sequences) against a database of 1 billion amino acids from the NCBI nr database using default NCBI BLAST parameters. By adjusting these parameters, we achieve even greater acceleration. Additionally, we accelerate all flavors of BLAST including nucleotide (BLASTN), protein (BLASTP), and translated versions (BLASTX, TBLASTN, and TBLASTX) with similarly impressive results. Our Tera-BLASTN performance numbers well exceed 1 million Giga-cells per second.”

For over 15 years, TimeLogic’s DeCypher systems have been at the forefront of accelerated sequence comparison by combining FPGA technology with high-performance servers to accelerate optimized implementations of BLAST, Smith-Waterman, HMMER and gene modeling algorithms. “We are very excited about the projects we have ongoing. In addition to updates to our existing algorithm modules, we’re also introducing an accelerated Short Read mapping algorithm intended for the analysis of Next Generation Sequencing data, which we’re confident will be a big hit,” continued Murray. Ted DeFrank, President of Active Motif also added, “The TimeLogic brand is the one of the original pioneers in the field of accelerated bioinformatics. The heavy investment Active Motif is making in this portion of our business will further strengthen our position as the world leader in providing accelerated tools for protein and DNA sequence comparison for Life Science Researchers.”

About TimeLogic

TimeLogic, a division of Active Motif, Inc, is the world leader in hardware accelerated bioinformatics search tools. Our accelerated genome annotation tools combine optimized bioinformatics applications with powerful FPGA-based PCIe accelerator cards. This blend of specialized hardware and optimized software provides a perfect combination of performance, accuracy and value. Furthermore, these systems are simple to maintain and scale easily. Utilizing a TimeLogic system reduces pressure on over-used CPU-clusters by off-loading BLAST, Smith-Waterman (SW) and Hidden Markov Model (HMM) tasks to a highly time and energy efficient solution. From the earliest genome sequencing projects in 1997 to the largest Metagenomics projects undertaken to date, TimeLogic has provided the enabling technology to make this research possible. Active Motif/TimeLogic operates globally through its corporate headquarters in Carlsbad, California, European headquarters in Rixensart, Belgium and Japanese headquarters in Tokyo, Japan. Active Motif/TimeLogic applies a multi-disciplinary approach to create new and modify existing technologies to meet the current and future needs of life science researchers.

Find out more by visiting us at http://www.timelogic.com or contact Michael Murray at tlsales@activemotif.com.

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