Setting Up and Running a Custom BLAST Server: A Comprehensive Guide

Molecular biology, bioinformatics, and genomics are fast-moving fields. Appropriately leveraging powerful tools like BLAST is essential for success. Here, we walk through some of the things you need to consider when setting up and running a custom BLAST server.

When is a custom BLAST server needed?

Why not just use NCBI BLAST? In many cases, a custom server is required. This is typically either because you’re analyzing data that doesn’t exist at NCBI, or because you’re trying to improve your productivity.

Using a custom server to keep your data and analyses confidential and secure

If you’re working with unpublished or proprietary genome data, you can’t use NCBI’s web server - your data isn’t on it. Thus, you need to run a custom BLAST server. This also helps to protect your intellectual property: Housing unpublished data on your server ensures it remains confidential, safeguarding your intellectual property. Running searches on your own server also means nobody can know which gene targets you are searching for.

Using a custom BLAST server can improve your productivity

Challenges to consider when setting up and running a custom BLAST server

Some parts of running your lab’s or department’s own BLAST server are easy. But there are challenges, too.

Keeping databases and software up-to-date

Such updates can be time-consuming and, if not done correctly, can lead to errors. Thus, it’s essential to have a plan for how to keep your databases and software up-to-date. This can be a challenge in small labs due to staff turnover and the lack of a dedicated bioinformatician. In well-funded core facilities, such routine work takes up valuable time.

Accessing the server from home and when at conferences

Where will you run your server?

Imagine you have a server in the lab.

How will your team members access it from home or when you’re at a conference?

What happens when the power goes down? Power outages are rare but also inevitable. A server losing power gets corrupted. A backup power supply (UPS) can keep your server running. You’ll also want an automatic shutdown script to shut down your server safely when the power goes out. Who will start it up again when the bioinformatician is on holiday? Automation and good policies are essential.

What happens if the server crashes? Perhaps because someone submitted a search that is too big. You really don’t want that to happen when you’re preparing for a conference, and nobody is there to get it running again.

Using a cloud BLAST service can solve these problems.

How will you keep your server secure?

If you’re running your own machine, you’ll need to have a plan for several elements:

What are the hardware requirements for running BLAST? What size server do you need?

The needs very much depend on what your usage is. Is it just you or many users (a lab, an institute, or a community?)? How often will BLAST be run? What types of queries? How many queries at once? How big are the queries? How big are the databases?

BLAST runs faster if it can load the whole database into memory (RAM). BLAST runs faster if using multiple cores (as long as the disk speed is fast).

How many simultaneous queries may occur? Can you keep them from overlapping? A 48-core machine with 512 GB RAM for running is superb for most labs. But buying and running that kind of machine isn’t cheap!

Our Cloud BLAST service is simple and reliable

Our SequenceServer Cloud BLAST service does away with the complexities described above.

People across pharma, biotech, and agroindustry trust SequenceServer Cloud Blast, as do many academic labs for teaching and research.

We’d love to help you, too.

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