MLST analysis

Multi-Locus Sequence Typing (MLST) using the BioNumerics MLST online plugin. See the MLST application page for a complete overview.

Different MLST trimming patterns using webservices

I have installed the MLST plugin with a scheme using webservices, and some of my stop trimming patterns are very degenerate. A colleague that installed it without webservices, has stop patterns that are perfectly fine. What is causing this difference?

MLST analysis starting from whole genome sequences

In this tutorial we will search for the sequences corresponding to the seven housekeeping genes used in the online MLST scheme of Listeria monocytogenes. The assembled sequences present in the whole genome demonstration database of Listeria monocytogenes are used in this tutorial.

MLST query sequences

FASTA file containing the first allele for each of the seven housekeeping genes from the Listeria monocytogenes MLST schema, for use with the Sequence extraction plugin.

Follow-up analysis of MLST data

In this tutorial you will learn how to perform some cluster analyses (UPGMA tree, minimum spanning tree, maximum parsimony tree, ....) on MLST data. You will also learn how to alter the layout of the clusterings and how to export the pictures to use it in a publication, presentation, etc.

Setup and analysis using a publicly available MLST scheme

In this tutorial the most common usage scenario of the MLST online plugin is illustrated, i.e. when you want to perform MLST using an already published MLST schema, made available via http://pubmlst.org or http://www.mlst.net or any other online repository. For many clinically relevant organisms, an MLST schema is already available and using this schema ensures a consistent nomenclature.

Setup and analysis using your own custom MLST scheme

This tutorial illustrates the steps needed to set up your own MLST schema, e.g. in case you are studying a less common organism for which no MLST data are available yet.

MLST plugin manual

In this manual you will learn how to install and use the MLST online plugin in your BioNumerics database.

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