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DELTA-BLAST

by A. Bretaudeau on May 31, 2012

Hi!

A new Blast version (2.2.26+) has been released by the NCBI a few weeks ago. You can now use it using our blast web interface, or directly on our cluster.

I have also updated the Symfony bundle (GenouestBlastBundle) to work with this new version, so if you are using it and willing to update to this new blast version, don’t forget to update the code.

What’s new

As usual, the blast+ changelog is available online.

Apart from a few bug fixes and improvements, the main changes concern the psi-blast output which is now available in all formats (txt, html, tabular, asn, …) and a new application: DELTA-BLAST.

DELTA-BLAST

DELTA-BLAST (Domain Enhanced Look-up Time Accelerated BLAST) is a new application to perform protein-protein queries with better sensitivity.

There is an article describing how it works.

Briefly, DETA-BLAST performs a multiple sequence alignment of the query sequence with domains described in the CDD (Conserved Domain Database from NCBI) database and then uses a PSSM derived from this alignment to search a sequence database.

The difference with PSI-BLAST is that PSI-BLAST uses the results of a first blastp iteration to construct a PSSM and then uses it to search the sequence database. DELTA-BLAST uses PSSM derived from the CDD database, so the initial PSSM construction is much more quicker than PSI-BLAST.

The results in the paper look promising. You can try it if you want to find sequences distantly related to your query sequence.

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