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Using eBURST


Version 3 is implemented as a JAVA Web Start application.
On first launching, eBURST will be downloaded and installed on your local machine, and will not need downloading again unless the software has been updated. Web Start allows data to be streamed directly from a website to the locally installed application significantly decreasing the amount of data transferred compared to previous versions.
This also allows eBURST to be used as a standalone application and details of differing usage methods can be found here

The interface to the eBURST application is split into three sections –
• The Profiles window.
• The Analysis window.
• The Diagram window

Each of these are accessible via ‘TABS’ within the interface, and each of the windows contains menu options, a main window and a panel containing context sensitive functions based on which window you are viewing – see Figure 5.

 

Figure 5

The Profiles window

The data used by eBURST is a list of STs and their allelic profiles. Data can be entered by ‘cut and paste’ and should be tab-delimited (or space-delimited) text, each line having the ST number followed by the allele numbers at the seven MLST loci (in the standard order of loci for the MLST scheme).

An example of correctly formatted input text is shown below:

233 2 4 5 6 7 8 9
88 1 1 1 3 7 23 11
54 12 3 43 32 9 11 3
213 21 22 4 38 5 23 8
54 12 3 43 32 9 11 3

eBURSTv3 is integrated within the mlst.net databases and can be launched after querying the database to examine subsets of a population, or can be launched to view the entire population of a particular species.

The option also exists to combine your own data, added by ‘cut and paste’ or upload, with all of the data that is in a MLST database. On clicking an eBURST button, the output from the database query, the whole database, or your data is sent to eBURST.

HINT – you may wish to use eBURST to compare your own isolates with all of the isolates of the species in the MLST database, but your MLST data may have alleles and/or STs that are not in the MLST database. These isolates can still be analysed by eBURST as they can be given temporary allele numbers (we suggest numbers above 1000 to avoid any confusion with the official allele numbers) and temporary ST numbers (we suggest greater than 10,000). Note that these numbers are just to allow you to analyse your data using eBURST and should NEVER be used in any publication (new alleles and STs should be submitted to the curator of the appropriate MLST database for official allele number and ST number assignments).

On submitting the data, eBURST will be launched and the data will appear in the ‘Profiles’ window. Once the data is loaded it can be sorted by ST number or by allelic profile using the ‘Profiles Menu’. Sorting by allelic profile is not optimised and sorts by the allele number at the first locus, then at the second locus, etc.

The ‘Open’ button in the ‘Profiles Menu’ allows a file to be uploaded and this option, or ‘cut and paste’ within the MLST website, allows any MLST data to be analysed by eBURST. The uploaded data will replace any data already in the Profiles window. Uploaded files must be correctly formatted text files, as in the example above.

eBURSTv3 has been developed and is hosted at Imperial College London