DeCypher
          Products    News    Support    Sales    Contact 
  bioinformatics and text mining solutions

Site Search:  

Section Topics:

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

News:

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

TimeLogic welcomes new customers at NIEHS, University of Sydney, Life Biosystems and Max Planck

DeCypher 7.6.2 software update improves HMM analysis, output formatting

Newsletter:

Subscribe to the TimeLogic newsletter for product information, special offers and technology whitepapers!

Signup

 

 

Tera-BLAST™

The ubiquitous nucleic and protein homology search tool, just faster

BLAST is a critical algorithm with broad applications from genome analysis to SNP mapping and proteomics research. With its heuristic design, it delivers results faster than dynamic programming methods such as Smith-Waterman. And yet the tremendous volumes of data generated by next-generation sequencing platforms can lead to days or weeks per BLAST search—even on a large cluster.

Several software implementations of BLAST exist from NCBI, Washington University and others. Tera-BLAST is a faithful implementation of BLAST software that executes on the TimeLogic FPGA-based NextEngine accelerator. Tera-BLAST derives its name the trillions (tera) of cell comparisons per second that can be accomplished on the TimeLogic solutions.

The Tera-BLAST algorithm suite is included with the CodeQuest workstations and is an available module for the DeCypher Enterprise solutions, where it complements the other sequence comparison modules, including HMM, SmithWaterman, GeneDetective.

Tera-BLAST Advantages:

  • Provides the performance of hundreds of modern CPU cores
    in a small-footprint solution

  • Higher throughput means you can complete better annotations with standard BLAST methods (BLASTN, BLASTX, TBLASTN, TBLASTX, BLASTP)

  • Can be deployed in a desktop computer, or installed across a DeCypher cluster of 20 nodes

  • "Nearly exact match" parameters enable anchoring on very small nucleic patterns (using nucleic wordsize as low as 4)

  • Includes Tera-Probe for mismatch-tolerant high-sensitivity oligo searches

  • Tera-BLAST delivers fast, affordable genome-scale analysis to your labor entire institution

Tera-BLAST™ Search Methods

Algorithm
Query/
Database
Description
Applications
Tera-BLASTN NT/NT Fast nucleotide search, find very similar matches, ungapped search
  • map 454 reads, EST or cDNAs onto a genome
  • identify overlaps for assembly workflows
  • running genome to genome comparisons
Tera-Probe™ NT/NT Compare oligos (up to 50bp) to genomic DNA with near-Smith-Waterman sensitivity
  • Identify potential microarray probes
  • Map short reads to a genome with up to 5 mismatches
  • Map SNPs to a genome with high sensitivity
Tera-BLASTP AA/AA Fast AA search, find easy homologous sequences, ungapped search
  • assign tentative functions
  • homology modelling when a match to protein with known 3D structure is found
Tera-BLASTX NT/AA Translate query in all 6 frames, search in AA space., ungapped search
  • assign tentative functions to novel cDNAs or EST
Tera-TBLASTN AA/NT Translate target in all 6 frames search resulting AA sequences, ungapped search
  • map proteins onto genome
Tera-TBLASTX NT/NT Translate query and target in all 6 frames, search the AA sequences, ungapped search
  • compare genomes, more sensitive for comparing coding regions

Custom Benchmarks

Contact us today for a sample Tera-BLAST benchmark on your data!

 

TimeLogic is a brand of Active Motif, Inc. All text © 2008