A procedure to derive the amino acid sequence from coordinates taking into account missing residues. This improves sequence homology searches due to avoiding gap penalties. Better scores lead to more reliable homology detection in blast.

See also: http://www.moltalk.org/PDBChainSaw.html

pdbchainsaw.png

On top of this sequence database we run a weekly blast all-against-all (Blast4All) to determine the homology relationships between structural chains. The results are stored in a relational database and made available through the iMolTalk server (click on a chain and select "Sequence Homologs" from the pop-up menue).

The results of the weekly blast all-against-all also forms the basis for a procedure to reduce sequence redundancy in the database.

We provide databases at the levels of 50%, 60%, 70%, 80% and 90% sequence redundancy thresholds.

Inspect the growth of the PDB in our chart of structural chains:

PDBChainSaw-Redundancy-Reduction.png

(note that there was a change of the blast version installed, which broke the XML result parser temporarily.)