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• Introduction
  • What is MLST?
  • The concept of the Multilocus Sequence Typing Module
  • Acknowledgements
• MLST quick-start
• Handling MLST schemes
  • Downloading schemes
    • Download custom schemes
  • Creating new schemes
  • Merging schemes
  • Viewing schemes
    • Profile table
    • Allele table
• Isolates
  • Assemble and create isolate
  • Working with isolates
    • Isolate-scheme dependencies and the sequence type
    • Opening contigs
    • Deleting contigs
    • Assigning new contigs
    • Align to nearest allele
    • Assemble to an existing isolate
  • View a report of an isolate
• Extending schemes
  • Add isolates to scheme
  • Add sequences to scheme
• Install and uninstall plugins
  • Installation of modules
  • Uninstalling modules
• Licensing requirements for the Multilocus Sequence Typing Module
  • Licensing modules on a Workbench
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Configure License Server connection
    • Download a static license on a non-networked computer
• Bibliography

Handling MLST schemes

An MLST scheme () consists of the following:

• Names of the loci to be sequenced.
• For each of these loci a list of the known alleles is maintained.
• A list of the known allelic profiles or sequence types described by the scheme.

Given this information, sequence data from a new isolate can be used to assign a sequence type.

In the Multilocus Sequence Typing Module, an MLST scheme can be created in two ways:

• It can be downloaded from a database, or
• Created from sequence data imported into the workbench.

The schemes downloaded from a database will already have information about many sequence types, whereas this information needs to be accumulated by the user for self-made schemes.

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Subsections

• Downloading schemes
• Creating new schemes
• Merging schemes
• Viewing schemes

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