Download MLST Scheme

To run the Download MLST Scheme tool choose:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Databases (Image typing_epi_folder_closed_16_h_p) | MLST Typing (Image large_mlst_open_16_h_p) | Download MLST Scheme (Image dl_large_mlst_16_h_p)

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Figure 16.5: The Download MLST Scheme settings.

Use the Schemes to download selector (figure 16.6) to choose which schemes to download from PubMLST.

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Figure 16.6: The schemes available for download.

Most of the schemes offered for download by PubMLST are classic (7-gene) schemes, but there are also core genome schemes available for several species, e.g.: Salmonella spp., N. gonorrhoeae, N. Meningitis, C. Jejuni / C. Coli, C. trachomatis, Vibrio cholerae, Listeria monocytogenes.

Some of the schemes offered by PubMLST may only contain allele and locus definitions and no sequence types.

The Download metadata option makes it possible to download and extract metadata for all of the isolates for a given species in PubMLST. Note that this is a potentially very slow operation.

The clustering parameters determine how the heatmap should be clustered (figure 16.7). The heatmap cellvalues are the observed frequencies of a given allele compared to the other alleles in the same locus.The possible cluster linkages are:

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Figure 16.7: The clustering parameters.

The possible distance measures are: Note that for schemes with thousands of sequence types and/or loci, the clustering may become very slow and time-consuming.

The following options are available when creating a minimum spanning tree (figure 16.8):

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Figure 16.8: The minimum spanning tree parameters.