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Using eBURST

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

In many cases eBURST will be used on output produced by querying a MLST database, or will input the whole of a MLST database. The option also exists to combine your own data, added by ‘cut and paste’, 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 ‘cut and paste’ is sent to the eBURST applet.

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 anayse your data using eBURST and should not 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, the eBURST Java™ applet will be launched and the data will appear in the applet ‘Profiles’ window. Once the data is loaded into the applet it can be sorted by ST number or by allelic profile using the ‘Profiles Panel’. 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 Panel’ of the applet 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.