About BLAST

BLAST is a well-known tool for comparing an input biological sequence against a database of sequences to identify regions of similarity.

Here, we implement BLAST to allow users to search their sequences against curated collections of genomic data hosted on our platform.

Why is it useful?

UNDER REVIEW ⚠️

BLAST helps researchers identify similarities between their query sequences and known sequences in databases, which can provide insights into function, evolutionary relationships, and potential annotations, for instance, AMR genes.

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 'BLAST' tool via Analysis tab.

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

STEP 4 Once you see the BLAST interface, input your query sequence and configure the search parameters as needed and hit SEARCH.

UNDER REVIEW ⚠️

BLAST interface where users can input their query sequence and configure search parameters.

Where to find out more?

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

There is more detailed information about BLAST 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