Sequedex classifies DNA sequences:
Who they came from and What they do
- 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.
Who's there? A bunch of viruses! Viral metagenomes from a set of patients with diarrhea. It looks like the cause of their illness was an enterovirus. Data courtesy Dr. Charles Chiu, UCSF.
What are those algae doing? Sequedex output from a series of algal transcriptomes under various treatments. The organism under study here, Chlorella, has no reference genome or transcriptome. Data courtesy Dick Sayre, LANL.
Complex communities, simple differences: People who have tooth decay show huge differences (>40 sigmas) in the frequency of genes that let bacteria live off sugars instead of nucleic acids. Blue dots are increased in caries, red is decreased. Data from NCBI SRA study SRP007831
Tissue differentiation by transcriptomes. Data from the MPSS atlas of human gene expression
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).
- 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.
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:
If the output of that command indicates you should update, do the following:
Sequedex is now installed. If you wish, you may add the bin/ directory to your path for convenience.
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
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 firstname.lastname@example.org. 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 email@example.com.
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.
- GenomeWeb article of October 9, 2012 entitled "LANL Seeks Commercial Partners for Microbial Genomic Functional Classification Software"
- LANL news release on Sequedex.
- Santa Fe New Mexican article on the Sequedex team.
- R&D Magazine recognized Sequedex as one of the 100 most significant inventions of the year with an R&D 100 award.
Press inquiries should be directed to James Rickman by e-mail or by phone at +1.505.665.9203.
- 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.
- NCBI genomes for bacteria, viruses, fungi, and protozoa (via BioMirror).
- MG-RAST metagenomics analysis/data server.
- Earth Microbiome Project site.
Software useful with Sequedex: