Create MLST Schemes
A scheme can be created from scratch by defining a number of loci and accumulating sequence information about each loci. The schemes have the same format as the schemes that are downloaded.
To create a new scheme, go to:
Toolbox | Microbial Genomics Module (
) | Typing and Epidemiology (beta) (
) | NGS-MLST (
) | MLST Schemes (
) | Create MLST Scheme (
)
This will bring up a dialog as shown in figure 12.3.
Figure 12.3: Entering basic information for the scheme.
In the top field you can enter a name for the scheme - typically the name of the species in question. Below, you can define the loci to be included in the scheme: type the name of the locus in the Name of gene field, and click the Add (
) button. If you accidentally add a wrong name to the list, select it and click the Remove button. When you are done adding loci for your scheme, click Next to start assigning sequences to the loci.
The wizard will open successively one window for each locus in the scheme (figure 12.4). In each of these windows, you can assign allelic sequences to each locus. In this example, the locus called gene1 from figure 12.3 has its own step where sequences can be added. Clicking Next will display a similar dialog for gene2, and so on for all the loci that were entered in the first dialog.
Figure 12.4: Selecting sequences for "gene1".
It is not mandatory to add sequences to the loci. You can also choose to proceed and create the scheme before you add sequences. If you just add individual sequences as shown in figure 12.4, they will not be combined in an allelic profile and the scheme will not yet contain any sequence types. See section extending_schemes about how to add Isolates to a scheme.