Technical information

This is the version 0.0.0 for the server.

We are currently indexing some of the annotated DNA in public databases; we believe to be capturing most of the well-annotated microbial sequences. Do not hesitate to contact us if we appear somewhat optimistic about that.

Having that said, this is a proof-of-concept and as such the content of the database is not restricted to bacteria. The best is to throw DNA at it and see by yourself what the outcome is like.

For a glimpse of what is referenced, check here.

Further details can be found in the publication http://dx.doi.org/10.1371/journal.pone.0083784

Requirements

This service is like a DNA search engine. It relies on both a server on our end and a client on your side. The client you are using is a javascript-enabled and HTML5-compliant web browser.

At the time we developed the site it was working for the following browsers and operating systems (blue areas):

Firefox Chromium Chrome Opera Safari IE
Linux
OS X
Windows
Android
iOS

Programmatic access is demonstrated in our Python client.

Usage

  1. Upload DNA sequences (FASTA or FASTQ formats)
  2. See what known DNA is it related to

We have short visual demonstration where we use Tapir with an Android tablet to analyze raw reads from Ion Torrent sequencing:

Example of result

  • icon Rotavirus A
    75% Match
    25% Match
    Full genome of the fictitious virus 123 (remember, this is an example)
  • icon Rotavirus F
    25% Match
    15% Match
    Full genome of the fictitious virus 456 (remember, this is an example)

The result is a vertical list of sorted matching references (here 2 references).

For entry in the list, that is each reference, the upper horizontal bar represents the amount of unique DNA in the query that is found matching that reference. If all the query DNA is found matching that reference, the bar will be the longuest.

The lower bar represents the fraction of the reference that the DNA in the query is found matching. The shorter the bar, the smaller the fraction of the reference found matching. If the full reference is present in the query DNA, the bar will be the longuest.

Credits and contacts

  • Laurent Gautier (laurent at cbs.dtu.dk)
  • Ole Lund (lund at cbs.dtu.dk)

Acknowledgements

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