DeCypher<sup>®</sup> Product Modules


Accelerated BLAST

Tera-BLAST is the best performing accelerated implementation of the BLAST algorithm on the market today. As sequencing technology continues to evolve, keeping up with the data analysis burden becomes more and more challenging. Whether you're utilizing high-throughput genome annotation pipelines, conducting large sequence database searches, or analyzing vast amounts of metagenomics data, our accelerated BLAST algorithm will allow you to process huge data repositories in record time. And our DeCypher solutions scale easily so increasing throughput is a quick, simple affair.

DeCypher FPGA vs. GPU

Alternative Graphic Processing Unit (GPU) cards can be used for a variety of computational tasks however algorithms with serialized or branching logic (i.e. Heuristic algorithms) tend to perform poorly on GPU cards. 

Tera-BLAST Performance White Paper

Recently we compared our Tera-BLAST algorithm, running on the TimeLogic J-series FPGA Similarity Search Engine, against Cuda-BLAST running on NVIDIA Tesla M2090 GPU cards and NCBI BLAST+ running on standard Intel Xeon (E5-2690) multi-core CPU’s and found that Tera-BLAST runs hundreds of times faster than either solution. Specifically, our FPGA-accelerated Tera-BLAST algorithm can provide the equivalent performance of 41 Dell R720 Servers (each with 32 CPU-cores). If you're looking for accelerated BLAST performance, look no further.

Download a copy of our Tera-BLAST White Paper, which details the performance difference between these different BLAST implementations.

With Tera-BLAST™, you can rapidly process BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX and Tera-Probe™ searches using our FPGA accelerator cards.  Our Tera-BLAST™ employs the same heuristics and scoring regime to achieve similar results to NCBI - albeit with much better performance.  

Please contact us today for customized performance benchmarks so you can assess the benefits of our solution.

Tera-BLAST™ Advantages:

  • Rapidly searches large databases (even full Genbank) for nucleic or protein matches.
  • Offers a wide range of sensitivity for flexible homology comparisons.
  • Compares evolutionarily divergent sequences using frame-translated searches.
  • Includes flexible alignment options to streamline your annotation tasks.


For sensitive, genomic mapping of short-read data and oligonucleotides

Tera-Probe™, part of the Tera-BLAST™ suite, combines the performance of Tera-BLAST[1] with efficient Query-Global Smith-Waterman alignment to identify oligonucleotide sequences across a genome. Tera-Probe™ exceeds NCBI BLAST[2] sensitivity and matches Smith-Waterman[3] results, yet offers much greater throughput.

Our DeCypher® biocomputing systems process Tera-Probe™ at a much higher rate than software Smith-Waterman (SSEARCH), making our solutions ideal for research teams designing microarray probes, mapping SNP databases and designing RNA interference experiments.

Sensitive Remapping of Short-Read Sequence Data

Tera-Probe™ is an ideal tool for secondary mapping of next-gen sequence data. Existing algorithms are sufficient to map exact matches, and 1-2 mismatch 36-mers to the genome, but by remapping with Tera-Probe™, you can increase the overall number of mapped reads due to higher tolerance for gaps, insertions and mismatches. This saves time, sample prep costs, and makes your sequencing process more efficient. Selecting Optimal Microarray Probe Sequences

Comparing short sequences to a genome database is essential for minimizing non-specific hybridization in microarray probe design. Tera-Probe™ offer significant advantages compared to other oligo search methods.


  • Often used to screen potential probe sequences, as it comprehensively explores all possible pairwise alignments to select an optimal local alignment.
  • Smith-Waterman software (SSEARCH) is slow even on fast CPUs, with processing limited to 30 million cell comparisons per second per CPU.


  • Uses heuristic shortcuts to focus on anchor regions that share some core similarity, resulting in faster searches at the expense of sensitivity.
  • May miss hits when multiple short gaps or mismatches occur between anchor regions


  • Processes oligonucleotide search pipelines at 330 billion cell comparisons per second, or thousands of times faster than Smith-Waterman on one CPU core.
  • Requires only the space, power and cooling of a single workstation or server.
  • Can be scripted into your analysis pipelines.
  • Forces the entire oligo query to align to local target loci to ensure that all potential hybridization sites are examined.
  • Matches the sensitivity of Smith-Waterman software.
  • You can employ a custom scoring matrix to establish finely tuned scoring for matches and mismatch penalties.
  • Included with the Tera-BLAST™ module for DeCypher®.

1. Luethy et al. Hardware and software systems for accelerating common bioinformatics sequence analysis algorithms. Biosilico 2(1), 2004.

2. Altschul, SF, et al. Basic local alignment search tool. J Mol. Biol. 215(3), 1990.

3. Pearson, WR. Effective protein sequence comparison. Methods Enzymol. 266, 1996.