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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.
Plot showing discrimination among human tissue types by functional classification of transcriptome data.

Updates

9 Jun 2014

Full Tree of Life, viruses, writes FASTA, 6 month demo license, plots.

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 , dated
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Choose your OS:

Trees

  • Life2550: a full Tree of Life including bacteria, archaea, and eukaryotes with classifications from SEED.
  • virus1252: a tree of viruses of all types (but excluding phages) with classifications from Pfam.
Sequedex classifies DNA sequences:
Who they came from and What they do

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.

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.
  • A 64-bit Java 1.7 or later run-time installed. The Java 1.6 distributed with Mac OS X is not acceptable. Desktop users may download Java from the java.com website.
  • A 64-bit Python 2 distribution with working SciPy installed (2.5 or later, but tested under 2.7). The python distributed with Mac OS X 10.9.2 (Mavericks) or later is acceptable; we recommend that you upgrade to the latest OS, but if you cannot do this for some reason you can install a 3rd-party python distribution. Desktop users may download a free and complete python distribution (Anaconda) here. Windows users must install Anaconda in the default system location.
  • 1 GB of disk space is required for download, installation, and testing.
  • 4 GB of RAM. However, RAM is cheap and Sequedex will use bigger data modules that identify more reads if you have 8, 16, 32, or 48 GB installed.
  • A windowing environment even on server systems to run the licensing GUI.

Installation

Make sure you have satisfied the System Requirements listed in the tab above before doing any further steps. Mac users will need to download Java and python as listed there, as the OSX-provided versions will not work.

Download the Sequedex distribution using the button at the right, and move the downloaded archive file to the directory where you wish to install Sequedex.

For now, installation is by command line on all platforms. Open a new command-line window (since an old one may not have the new java and python on the path) and issue the following commands, replacing the items in angle brackets with appropriate values for your system:
% cd <path to sequedex-archive>
% tar xzf sequedex-<version>-<platform>.tgz
% cd sequedex
If your network is behind a proxy server, do the following:
% bin/sequedex-config http_proxy <your proxy>
% bin/sequedex-config https_proxy <your proxy>
% bin/sequedex-config no_proxy <mycompany.com>,localhost,127.0.0.1
Then check to see if your system can benefit from an update:
% bin/sequedex-changes
If the output of that command indicates you should update, do the following:
% bin/sequedex-bootstrap
% bin/sequedex-update

Sequedex is now installed. If you wish, you may add the bin/ directory to your path for convenience.

Obtaining a License File and Testing

You may obtain a free 6-month 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.

Free demo licenses are available for a 6-month period 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.

Once you have obtained a demo license, you may wish to test that everything is working properly. A set of test data has been provided for this purpose here (tar) or here (zip). Unpack the data, start sequescan, and click on the file chooser icon at the right edge of the Input line.  In the directory you unpacked the test files, select the sequedex.testdata directory. Then click the "Run Sequescan" button.  If you have not previously accepted the license, you will have to accept it, and click "Run Sequescan" again. Sequedex should return results indicating success within about 3 minutes. Click on on the "Run Sequinator" button to display the results.

Press


Press inquiries should be directed to James Rickman by e-mail or by phone at +1.505.665.9203.

Business inquiries should be directed to Rob Dye at LANL's Feynman Center for Innovation.

Upcoming Features

  • Open database writing code so you can roll your own.
  • 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.

Resources

Data sources:

Software useful with Sequedex:

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