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New BLAST+ web form

by A. Bretaudeau on February 2, 2011

Hi all,

Today, let’s talk about the famous BLAST and its successor BLAST+! BLAST+ is available on the platform.

At the beginning…

…there was BLAST. It was published in 1990 and it is one of the most used bioinformatics tools. Many web form has been created around the world, the main ones being at the NCBI or at the EBI. In short, if you don’t already know what is BLAST: it compares sequences and allow you to find sequences that are similar to a given one.

The main BLAST implementation comes from the NCBI, although other implementations were also released (WU-BLAST which was later renamed AB-BLAST and is not free, FSA-BLAST, …).

BLAST comes in many flavours (blastn, blastp, blastx, tblastn, tblastx, psiblast, phiblast, megablast, …) which mainly differ in the type of sequences that are compared.


At the end of 2009, the NCBI published a complete rewrite of their BLAST: it is now called BLAST+. Their aim was to provide a faster implementation, easier to use, and providing comparable results.

If you’re not using the command line, the main change you can see is the NCBI web interface that was completely revamped a few months ago.

At the command line level, there were many changes. In fact they renamed all the binaries and options. The following picture perfectly illustrates this:

At the top, the binaries of BLAST. At the bottom, their equivalent with BLAST+.

I think they decided that it was time to change all the names once and for all. And I think they’re right: it’s much more usable now. For compatibility, there is a perl script that you can use to translate an old command line into the BLAST+ format.

If you look at the publication, you’ll see the performance improvements.

BLAST+ at GenOuest

On the platform, we have installed BLAST+ (but the legacy BLAST is still available of course). To use it with command line, just source it like this: “source /local/env/envblast+”, and then you can play with blastn, blastp and all their friends.

If you prefer a web interface, we have created a new one using BLAST+. It is largely inspired from the NCBI form, the main differences being the available databanks, and the dedicated resources.

We hope you will like it. It is already much better than our previous form. We should improve it with a surprise in a few weeks.

Tell us if you have any problem with this new form!

From → Tools

  1. The new form looks great! Is it open source? 🙂

  2. Thanks!
    The code is not released (yet?). In fact I don’t know if anyone would be interested in getting it, but after all, why not?

  3. Yeah, for those of us who do in-house BLAST. Your form is much better than wwwblast!

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