START2 - Load profile definitions

The profile definitions for a MLST scheme are the complete set of known STs/allelic profiles. It is not necessary to load the definitions to work with your own dataset, but START2 can use them to fill in gaps in your dataset (e.g. if your dataset just had ST numbers but no profiles, the profiles can be filled in automatically by the software, and vice-versa).

The profile definitions can also be used as a dataset in their own right. To enable this, make sure that the 'Automatically create a dummy isolate dataset ...' option is selected when you go to 'Options → General'.

To load the profile definitions, select 'File → Open or Enter → Allelic profile/ST definitions'. This option will only become enabled once you have defined a scheme.

Enter the location of the profiles file in the 'File location' text box and press 'Load'. The location can be either on a local drive or a network resource (web or FTP site). If the location has been defined when you defined the scheme, this will already be entered. For schemes hosted on pubmlst.org, profile definition files can be found at http://pubmlst.org/data/.

Alternatively, you can click the 'open file' button on the toolbar and load a local file that way.

You may also copy and paste profiles from a spreadsheet.

At this stage, you can also check the integrity of the profile definitions. Make sure the 'check integrity' checkbox is selected and then press 'OK'. This tests to make sure that there are no duplicates or that two ST numbers are associated with the same profile or that a ST number is associated with two profiles. There is no need to check the integrity of profiles loaded from pubmlst.org, as these are guaranteed to not contain such problems.