Single genome seach

How to generate a context for a single genome

To create a collection of the genomic neighbourhood:

1. Click "View Cluster" to go to the cluster viewer

2. Select genomes you want to keep (or all of them)

3. Click the 💾 icon in the top right

Finding the context for a single genome

Using the Clustering Panel

Creating the clusters

The first time a genome is uploaded, it is often necessary to first run the clustering by clicking on the "Cluster Now" button. This can take a few minutes, depending on server usage and the size of the data set involved. If you're looking at an old record and new genomes are available, whether from public imports or your own uploads, you can search against these as well using "Re-cluster" button.

Navigating the embedded cluster view

Each node in the network represents one or more genomes with an identical cgMLST profile that either connect directly to the query genome at less or equal to the threshold or can be linked to it via a chain of connected genomes. The resulting network shows genomes linked to the query genome by fewer differences than the selected distance threshold (number of different alleles). This threshold can be modified using the slider under the chart showing the number of genomes at each value.

Dark purple: The query sequence and any other genomes with an identical cgMLST profile

Light purple: Genomes directly connected to the query within the threshold

Pale blue: Connected to the query by one or more intermediary genomes

This network can be opened in a Cluster View and the related genomes investigated ("View Cluster"). Alternatively the list of linked genomes can be opened in the Genome List view, from where detailed analysis downloads and tree-based collections are available ("List Genomes"). Note that you will need to click the "Clear Filters" button to reset the Genome List view afterwards.