SeqCruncher Accelerator

Products

Applications

News

Support

Sales

Community

Contact

bioinformatics and text mining solutions

Section Topics:

• Introduction
• SeqCruncher Accelerator
• Tera-BLAST
• Tera-Probe
• GeneDetective
• HMM Solution
• Smith-Waterman
• Algorithms
• Interfaces
• Configurations
• Published Citations

News:

Invitrogen and Active Motif explore use of FPGA for Next-Generation Sequencing Data Analysis

SeqCruncher™ improves DeCypher and CodeQuest throughput by 3-20X

TimeLogic welcomes new customers at NIEHS, Hiram College and the Korea National Institutes of Health

DeCypher 7.6.2 software update improves HMM analysis, output formatting

SeqCruncher™ PCIe Accelerator Card

Designed to handle the explosion of data generated by next-generation sequencing platforms, TimeLogic's SeqCruncher™ accelerator is an entirely new circuitboard design that leverages the speed of new Xilinx® FPGA chips and the PCIe data bus. The SeqCruncher delivers 3-15X better performance compared to our DeCypher Engine G4 (PCI-X) accelerator card. HMM tests completed on one SeqCruncher ran 550X faster than HMMer software tests completed on one 2.66 Ghz Xeon CPU core.

NextEngine

In addition to hardware performance upgrades, TimeLogic has re-engineered each algorithm suite to deliver peak performance for today's search bottlenecks. The SeqCruncher architecture enables us to run Smith-Waterman searches with oligo-length queries 10-fold faster than our DeCypher Engine G4 hardware. This is highly valuable for groups studying genomic signatures, identifying siRNA/miRNAs, mapping SNPS and short-read sequencing data to genomes.

We have completed over 400 performance tests to validate algorithm performance across multiple server types and algorithm conditions. SeqCruncher-based DeCypher systems have been validated on servers with quad-core Intel Xeon™ CPUs. We recommend Dell 2950 and HP DL380 models, each of which accomodate 1-3 SeqCruncher cards, as well as the Sun Ultra45 workstation. DeCypher can be installed under Windows 2003 server, RedHat Linux and Solaris 10. Additionally, the CodeQuest workstation is now available with 1 or 2 SeqCruncher accelerators for 3-30X better performance.

First Name
Last Name
Position
Institution
Country
Phone
Web Page
Email

Interest:

If you require pricing details, please specify the following options:
Include Tera-BLAST™ and Tera-Probe™ module
Include GeneDetective™ module for gene modeling
Include Smith-Waterman module
Include Hidden Markov Model (HMM) module
Upgrading from DeCypher Engine G4 solution

DeCypher Configuration:

Other DeCypher configuration request

Benchmark request (list query file details, database and parameters)