TimeLogic,
DeCypher<sup>®</sup> Product Modules

DeCypher® Product Modules

Accelerated Bioinformatics Algorithms and Other Features

DeCypher® systems are fully customizable genomic appliances that include one or more of our proprietary, J-Series  Field Programmable Gate Array (FPGA) PCIe cards along with one or more of our optimized algorithm modules. The current host-server for our DeCypher systems is the Dell R720, which will accommodate up to 2 of our J-Series FPGA cards. Customers can choose any of the following optimized algorithms for use with their DeCypher system®.

Algorithms Modules

  • Tera-BLAST™ is ideal for rapid gene and protein annotation. Tackle huge EST annotation projects by comparing large batches of ESTs to databases like GenBank nt or Swiss-Prot. Tera-BLAST is also ideal for mapping your 454™ sequence data to the genome. Tera-Probe™, part of the Tera-BLAST™ module, uniquely combines sensitivity and performance for oligo searching. Standard Tera-BLAST can map 500,000 oligos (exact match) per hour, but if you need near-Smith-Waterman sensitivity, Tera-Probe let's you compare 10,000 per hour at high sensitivity. This makes it ideal for short sequence reads, SNP mapping, locating potential microarray probes and primers, and for identifying off-target siRNAs. 
     
  • DeCypherHMM™ delivers blinding speed for Hidden Markov Model and ProfileSearch searches. Compare genes and proteins to PFAM, TIGRfam and Superfamily to identify protein families. Or, compare your HMM models to protein sequence databases to see what new sequences fall into a particular family. 
     
  • GeneDetective™ allows you to model genes by mapping EST, cDNA, protein sequences—or even HMM models—to genomic DNA. The graphical output can help you investgate alternatively spliced cDNAs, and the multiple sequence alignments and putative transcript listing provide sequence-level detail for you to amplify specific splice variants.
     
  • Smith-Waterman and Framesearch are the de facto standards for robust cross-genome protein comparisons. CodeQuest® also includes Symmetric Framesearch (SFI) for frame-tolerant comparisons in both query and target database files to capture evolutionarily distant connections. 

Other Modules and Features

  • The Core Admin module includes enhanced functionality and is intended for facilities that service many users and groups and require additional levels of information security and management.
     
  • PipeWorks® is an intuitive software package that allows researchers to visually design and process powerful workflows. These workflows are easy to generate and edit, and can be easily shared among colleagues, without the need for tedious scripting.