454 & Ion Torrent Data Analysis

Is your data piling up while you wait for cluster time?

DeCypher® systems gives your lab the power to rapidly annotate 454 or Ion Torrent data without having to rely on overtaxed clusters and harried IT staff. Find out how TimeLogic can help and schedule a free benchmark on your 454 or Ion Torrent data!

8 ways a DeCypher® system can improve your 454 or Ion Torrent analyses:

  1. Align reads, contigs or scaffolds to your reference genome using Tera-BLASTN™, which offers a wide range of sensitivity and alignment options. You can even specify NCBI output format to leverage existing parsers and analysis workflows.
  2. With any DeCypher® search, you can generate alignments with 100-1000+ bases of additional upstream and downstream sequence for further exploration of your alignment context within the genome.
  3. Identify putative transcripts by mapping reads to genomic reference using GeneDetective™, which takes into account canonical splice sites in it's alignment phase. GeneDetective is also useful when identifying orthologs from large sequences that include many introns.
  4. Short indels and homopolymer errors can make some 454 or Ion Torrent reads hard to align and can complicate your gene prediction efforts. To overcome frameshift errors, DeCypher™ includes FrameSearch, which spans reading frames in the query or reference database (or both, using the Symmetric Frame Independent™ option).
  5. Compare translated reads or contigs to UniProt using Tera-BLASTX™ or Tera-TBLASTX™ in order to identify related proteins. A single DeCypher FPGA card runs Tera-BLASTX™ searches 100-200X faster than NCBI BLASTX on one CPU core. That's like having 12-24 screaming 8-core servers on your desktop, just without the noise, heat and 48 power cords.
  6. If you're interested in novel gene discovery and metagenomics, DeCypher® can rapidly find matches to protein families by comparing 454 or Ion Torrent data to PFAM using Hidden Markov Model searches. In addition to standard nucleic-to-HMM searches, DeCypher also offers HMM-Framesearch to accommodate common homopolymer data errors.
  7. Once you've turned raw sequence data into protein-level knowledge, DeCypher's intron-tolerant Double Affine Smith Waterman searches let you handily compare entire proteomes.
  8. The PipeWorks® graphical workflow tool lets biologists design and execute their own next gen workflows. This Windows application enables drag-and-drop design of workflows using TimeLogic's FPGA accelerated tools and can be installed on systems running Microsoft Windows.