Skip to content
Switch branches/tags
Go to file
Cannot retrieve contributors at this time

BLAST tutorial with Jupyter Notebooks and Command Line

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. Using command line and Python-based features, we can do even more with BLAST. In this tutorial, we demonstrate how to use some of these features. We will use Jupyter notebooks that work in-browser, allowing you to skip setting up the proper environment locally.

Before you launch the Jupyter notebook, note that:

  • They might take a few minutes to launch. You can click the "show" button to the right of "Build logs" to see the launch progress.
  • The notebooks will not work in Internet Explorer or Microsoft Edge. Please use a different browser, such as Google Chrome.

Click the launch binder button below to launch the Jupyter notebook.



This tutorial is largely taken from Wayne's Bioinformatics Code Portal's Blast Binder. Most of the code and readme is from this source. It is your responsibility to ensure that your usage of software is in compliance with all applicable usage requirements.

The BLAST software is available directly from the National Library of Medicine under BLAST+ executables.

The BLAST software references are listed here.

NCBI has made available an Amazon Machine Image (AMI) that will generate a remote cloud compute instance already set to run standalone BLAST, see here. Additional documentation is here.

More on BLAST:

Technical Details

This repository is set up to make use of the binder service offered by

It was developed from combining much of the binderized repo here with the ability to also run PatMatch. Click here for information about PatMatch and launchable Jupyter notebooks demonstrating its use.