About Gene Presence

Gene Presence is an analysis tool to determine whether loci (regions) in a genome are present or absent, incomplete, have alleles designated, or sequence regions tagged for selected isolates and loci.

Here, we implement Gene Presence to allow users to analyse gene presence across curated collections of genomic data hosted on our platform.

Why is it useful?

UNDER REVIEW ⚠️

Gene Presence helps researchers determine the presence or absence of specific genes across different isolates, which can provide insights into genetic diversity, pathogenicity, and resistance mechanisms.

Some use cases include ...

How to use it?

STEP 1 Go to the collections page to select the organism's database you want to search against.

Selecting a collection to search against.

STEP 2 Log in using your PubMLST credentials.

Logging in button highlighted in red on the overview page of selected collection.

Main collection login page. Use PubMLST credentials.

Overview page of selected collection after logging in.

STEP 3 To access the tool's page, either click on the Analysis tab to display a link or find a button to the plugin at the bottom of a search results.

Accessing 'Gene Presence' tool via Analysis tab.

Accessing 'Gene Presence' tool via button at the bottom of search results.

STEP 4 Once you see the Gene Presence interface, select the isolates/loci set, choose detection options, and run the analysis.

UNDER REVIEW ⚠️

Gene Presence interface where users configure loci detection parameters.

Where to find out more?

Gene Presence is implementated as part of BIGSdb, the software powering PubMLST.

There is more detailed information about Gene Presence and its different parameters here.

Contact us

For queries and to report any issues, email us at: email[at]biology.ox.ac.uk

Ineos Oxford Institute for antimicrobial research

University of Oxford

Sir William Dunn School of Pathology

South Parks Road

Oxford, OX1 3RE

United Kingdom