SeqNFind™ – Bioinformatics Software Tool
SeqNFind™ is a powerful tool suite that addresses the need for complete and accurate alignments of many small sequences against entire genomes utilizing a unique hardware/software cluster system that leverages a multi-processing Nvidia Tesla™ environment to do fast and complete short read genomic sequence alignments. SeqNFind™ utilizes a database linked cross-platform, graphical user interface based toolset for facilitating bioinformatics research in:
• Next Generation Sequencing

• Genomic comparisons


The amazing SeqNFind™ toolset can be used for:
• Smith-Waterman: Unlike many implementations such which start with a heuristic or use large tiled target sequences, SeqNFind™ provides the user with an accelerated manner in which examine to all locations within a genomic alignment. This tool allows comparison of every genomic base as an individual affine gap alignment. The system uses an accelerated Smith-Waterman to examine short read local alignments, returning a filtered set of viable patterns and locations.
• BLAST: SeqNFind™ provides GPU cluster enabled implementations of the standard BLAST tools for nucleotide sequence comparison.
• Reference Assembly
• De novo Assembly
• HMM
• Needleman-Wunsch
• RNA-Seq


What makes SeqNFind™ Unique?
SeqNFind™ is based on NVIDIA Tesla GPU hardware that can be affordably scaled, unlocking the huge potential of the Graphic Processing Unit (GPU). GPU computing is the future and uses GPUs to do general purpose scientific and engineering computing. GPUs contain hundreds of cores which can easily be scaled to outperform clusters, not only saving significant time, improving accuracy, but also using much less electrical energy.

The schematic shows the comparison of CPU versus GPU, a 60fold increase in the number of processors over a CPU. In many cases the product cost will have a rapid ROI based on the savings in power costs alone, when compared to traditional genome comparison methods using clusters.
If you need to accelerate your bioinformatics research without losing accuracy, please call us.
To contact a sales representative or to learn more about this exciting new bioinformatics tool please call 800.565.5467 or 910.673.8165 (outside the US and Canada).

 

 

 

 

Hardware Configuration

 

SeqNFind™ Workstation comes as a low-cost, single user, turnkey solution workstation with four NVIDIA Tesla C2050 GPUs. The system is a 4U Workstation with two Intel Westmere CPUS, 24 GB of 133 MHz DDR3 ECC RAM, 6 TB, 7200 RPM disks pre-loaded with Open Source Linux and the SeqNFind™ Workbench.

 

 

 

 

 

 

SeqNFind™ Compute Node comes as a cluster ready compute node. It can be integrated into existing clusters or as part of a dedicated, turnkey cluster. Each node contains two NVIDIA Tesla C2050 GPUs, two Westmere CPUs, 24 GB RAM, 1 TB of disk space and 5 user licenses. Up to 1,000 compute nodes can be added together for an equivalent of 896,000 cores!

 

 

 

 

 

BRC 2013 Presentation:
Burrows-Wheeler Mapping and SeqNFind®: A Comparative Analysis of Genome Mapping Tools
D. Andrew Carr
Triangle Biotech Research Symposium, Raleigh, NC 8/20/13


Nvidia GTC 2012 Presentation:
SeqNFind®: Application of Sequencing Alignment Techniques to CUDA GPU Technologies
D. Andrew Carr
Accelerated Technology Laboratories, Inc. 496 Holly Grove School Road West End, NC 27376 and University North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223.


ISMB 2011: Presentation:
Flanking Sequence Effects on Oligonucleotide Hybridization.
D. Andrew Carr*, Saeed Khoshnevis, Donald Kolva* and Jennifer Weller
*Accelerated Technology Laboratories, Inc. 496 Holly Grove School Road West End, NC 27376 and University North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223.


ISMB 2010: Presentation:
A Computational Study of Cross-hybridizing Stable Loop Structures in Oligonucleotide Sequences.
D. Andrew Carr1, Saeed Khoshnevis2 and Jennifer W. Weller2
Accelerated Technology Laboratories, Inc. 496 Holly Grove School Road West End, NC 27376 and Bioinformatics/Computer Science, University North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223.


• Article: "Speeding Toward the Future of Medicine"
Read about ATL's exciting new SeqNFind® Product in the article on the NVIDIA website: http://www.nvidia.com/object/gcr-genomics-research.html

Read all about SeqNFind® in Nature (August 2011)