Performing BLAST analyses in the Cloud

Cloud cluster for faster analysis - Datacenter photo credit Hyacinthe C -

So you’ve got a few sequences you want to BLAST search against a database, and you want to get the results as quickly as possible. Perhaps you’re trying to find sequences of new genes or to check primers. Sometimes the NCBI BLAST website just isn’t appropriate…

Why you might want to use the Cloud to run BLAST analyses

There are three main scenarios in which you’re likely to want to run BLAST in the cloud.

Scenario A: you have unpublished or proprietary databases that are not available at the NCBI BLAST website.

Scenario B: you’ve been running BLAST on your local computer, but:

Scenario C: you could run blast on your high performance computing cluster (HPC).

Scenario D: you’re tired of waiting for NCBI BLAST, or want to submit larger queries than what it will support. Sure it’s free, but your time is precious and you need to get things done.

Scenario E: you’re trying to protect your company’s intellectual property, and want to avoid sharing your search queries with the an agency funded by the US government.

Using cloud computing for BLAST analysis

By using cloud computing for BLAST analysis, you’re running BLAST on a server that should have much more computing power than the computer in front of you.

You can run the analyses through a web browser with a point-and-click interface, or in the command-line.

Mechanisms for running BLAST searches in the Cloud

If you’re happy to use BLAST in the command-line, you can set things up yourself on one of the major cloud computing platforms (e.g., OVH, Microsoft Azure, or Amazon Web Services), where you pay according to your usage. In particular, NCBI provide documentation and a BLAST+ Docker image to enable you to set up your own cloud computing environment for running command-line BLAST.

If you want a simple setup for running BLAST and prefer to use a graphical interface, you’ll probably prefer our SequenceServer Cloud solution. It makes BLAST analysis accessible through the web browser. Just point and click to set up BLAST, databases and permissions. SequenceServer Cloud uses the most recent and powerful versions of BLAST and SequenceServer, which provides many benefits for sensitivity, specificity, visualization and interpretation (the paper describing SequenceServer BLAST has been cited by hundreds of researchers and is used in labs and companies worldwide).

A SequenceServer Cloud instance for BLAST analysis can be private or publically available:

SequenceServer Cloud has a low monthly cost, and discounts for students, academics and yearly payments.

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