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Using MLST for bacterial typing

A bacterial “type” is a particular species with certain features.

  • For example, the bacterial type may be Staphyloccus aureus with resistance to penicillin.
  • To “type” a bacteria, we can focus on several genes, and see which allele is present for each of these genes.
  • Each bacterial species will have its own scheme, which is the set of genes that are looked at.
  • Overall, this process is called multi-locus (= several genes) sequence typing, or MLST.

In this tutorial, we will perform MLST on a bacterial sequence.

New to Galaxy? First try the introduction and then learn some key tasks

Get data

  • Log in to your Galaxy instance (for example, Galaxy Australia,

If you are using Galaxy Australia, look for the file we need in the Shared Data.

  • In the top centre panel, go to Shared Data
  • Click Histories
  • Click on the history named MLST-tutorial
  • Click Import (in the top right corner)
  • This should now be your current history.

Alternatively, we can get the sequence from Genbank.

This downloads sequence.fasta to your computer.

In the tool panel, go to Get Data -> Upload File

  • Choose local file: select sequence.fasta
  • Start
  • Close

This file should now be in your History panel. When it has completed uploading, the file name will be green.


In the tool panel search box, search for MLST.

  • Click MLST

The tool interface will appear in the centre Galaxy panel.

  • For input_file, choose the sequence file that you uploaded, e.g. sequence.fasta
  • Click Execute

What does MLST do?

  • Takes a fasta or genbank file
  • Scans this against all the typing schemes
  • Finds the best match (e.g. a scheme for the correct species)
  • Reports the output:
    • the scheme chosen
    • the sequence type (e.g. ST = 21)
    • the genes in this scheme and the alleles found in the data

View results

The results file will be at the top of your history panel.

  • Click on the eye icon to view the output.

  • Your results will be a single line.

For example:

  • Column 2: the scheme
  • Column 3: the sequence type
  • The rest of the columns: the gene names with the allele number in brackets. It is this combination of alleles that defines the sequence type.

In this example, our sequence type is ST=36. This is methicillin-resistant Staphylococcus aureus (or MRSA).

See this history in Galaxy

If you want to see this Galaxy history without performing the steps above:

  • Log in to Galaxy Australia:
  • Go to Shared Data
  • Click Histories
  • Click Completed-MLST-analysis
  • Click Import (at the top right corner)
  • The MLST analysis should now be showing as your current history.

What’s next?

To use the tutorials on this website:

  • ← see the list in the left hand panel
  • ↖ or, click the menu button (three horizontal bars) in the top left of the page

You can find more tutorials at the Galaxy Training Network: