`
Sequedex places DNA on the Tree of Life
Sequedex recognizes ATG (protein start) in DNA sequence
Vertical axis is the number of reads assigned; horizontal axis is the location on the phylogenetic tree of viruses.
Functional rollups show significant differences in gene frequencies transcripome of an organism that has not been its genome assembled.
Plot showing significant differences between groups; horizontal axis is phylogeny, vertical axis is function.  Red indicates significant decreases, blue indicates increases.

Updates

3 Oct 2012

Demo license server is up.

28 Sep 2012

Version 0.9.2 released.

17 Sep 2012

Site went live.

Download Sequedex

The current version is . Choose your OS:

Data Modules

  • Bact403: a one-per-genus bacterial tree, with functional classifications based on SEED.
Sequedex classifies DNA sequences:
Who it came from and What it does

Advantages

  • Analyzes collections of sequences in new ways, answering who is doing what? and bridging molecular to ecological scales of biology via evolution.
  • Extremely fast and resource-sparing. A single core of your laptop can be ~250,000X faster than BLAST and twice as fast as uploading your data to a cloud. Sequedex tames the data deluge that has been widely noted, bringing analysis costs back into line with sequencing costs without cloud security and outage issues.
  • Works for reads as short as 30 bp where other methods fail.  You don't have to distort your data through a non-linear filter like assembly just to get results. Linear and broad diagnostics enables ecological management strategies for tough problems.
  • Phylogenetic signature algorithm works for novel organisms, so you're not blind to microbes that aren't similar to those in genome databases. More sensitive to distant relationships than methods based on mapping methods.
  • We already built a Tree of Life for you, so your analysis doesn't have to wait on a team of bioinformaticians to finish their analysis first.

Potential Applications

Potential applications for Sequedex exist anywhere analysis of biological sequences (bioinformatics) may be informative, including:

  • ID of infectious diseases whether arising from bacteria, parasites, or viruses (medical, public health, biodefense).
  • Characterizing gut, oral, and skin microbiomes of humans, livestock, and pets (medical, pharmaceutical, veterinary, consumer).
  • Metagenomics of soils, rivers, oceans, foods, and process environments. (ecology, manufacturing).
  • Transcriptome characterization (medical, pharmaceutical, agricultural, biofuels).
  • Enzyme mining (chemical manufacturing, biofuels).
  • Cancer genomics (medical, pharmaceutical).
  • Companion diagnostics (pharmaceutical, agricultural, consumer care).

System Requirements

  • A computer with a 64-bit operating system such as Mac Snow Leopard or later or Linux 2.6 or later. We are still working on Windows packaging at this time.
  • A 64-bit Java 1.6 run-time installed. Mac OS will automatically install this for you. Linux users should consult their system documentation or download Java from here.
  • 1 GB of disk space is required for download, installation, and testing.
  • 8 GB of RAM. However, Sequedex can deliver acceptable performance with as little asi 2 GB of RAM if your swap space is on a SSD.
  • A windowing environment even on server systems to run the licensing GUI.

Installation and Testing

Download a package for your operating system at right, then follow the instructions in the online documentation.

To test that Sequedex is installed properly, in the open Sequedex application window, click on file chooser icon at the right edge of the "Input" line.  Select the testData directory you installed earlier, then select one of the files under "synthetic".  Click "Run Sequescan".  A few lines should appear in the "Progress" portion of the interface immediately. Sequedex should return results indicating success within a few minutes.

Obtaining a License File

You may obtain a free 60-day node-locked demo license by submtting a license information file by e-mail. A demo license will be returned to you immediately if one has not been granted for your e-mail or node ID before. Terms of the demo license are available here.

To create a license information file, start the Sequedex GUI and click on "Utilities->Request license".  Follow the instructions to generate a license information file.

Demo licenses are available for 60-day periods by e-mailing the license information file as an attachment to sequedex-demo-license@lanl.gov. A license file will be returned to you at the e-mail address you specified in the license information file.

One-year paid licenses are available at the special introductory rate of 1000 USD for academic users by contacting sequedex-license@lanl.gov.

Press


Press inquiries should be directed to Nancy Ambrosiano by e-mail or by phone at +1.505.667.0471.

Business inquiries should be directed to Rob Dye at LANL's Technology Transfer Divison.

Upcoming Features

  • Windows packaging.
  • Add-on data modules for non-bacterial parts of the Tree of Life.
  • Output of a searchable database of classified reads.
  • Publishing open-source database writing code so you can roll your own if you want.
  • Ability to characterize biodiversity (alpha diversity) of a metagenome using signatures.
  • Ability to characterize divergence (beta diversity) among metagenomes using signatures.
  • Ability to characterize sequencer performance as a function of position along reads.
  • User-defined functional classifications.
  • More downstream analysis scripts in python and R.
  • FASTQ reading and writing, handling paired-end reads.
  • Metagenomic signature calculation. Overlap-based assembly.
  • Amino-acid input and output (proteomics).

Resources

Data sources:

Software useful with Sequedex:

Operated by Los Alamos National Security, LLC for the U.S. Department of Energy's NNSA © Copyright 2012 LANS, LLC All rights reserved | Terms of Use | Privacy Policy | LA-UR-12-24796