Download Large MLST Scheme

To run the Download Large MLST Scheme tool choose:

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

Image lmlst_download_step1
Figure 18.5: The Download Large MLST Scheme settings.

Use the Schemes to download selector (figure 18.6) to choose which schemes to download from PubMLST.

Image lmlst_download_step2
Figure 18.6: 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 18.7). 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:

Image lmlst_clustering
Figure 18.7: 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 18.8):

Image lmlst_minspanningtree
Figure 18.8: The minimum spanning tree parameters.