%0 Journal Article
%T Domain enhanced lookup time accelerated BLAST
%A Grzegorz M Boratyn
%A Alejandro A Schaffer
%A Richa Agarwala
%A Stephen F Altschul
%A David J Lipman
%A Thomas L Madden
%J Biology Direct
%D 2012
%I BioMed Central
%R 10.1186/1745-6150-7-12
%X We describe a new method, called domain enhanced lookup time accelerated BLAST (DELTA-BLAST), which searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. For its PSSMs, DELTA-BLAST employs a subset of NCBI¡¯s Conserved Domain Database (CDD). On a test set derived from ASTRAL, with one round of searching, DELTA-BLAST achieves a ROC5000 of 0.270 vs. 0.116 for CS-BLAST. The performance advantage diminishes in iterated searches, but DELTA-BLAST continues to achieve better ROC scores than CS-BLAST.DELTA-BLAST is a useful program for the detection of remote protein homologs. It is available under the ¡°Protein BLAST¡± link at http://blast.ncbi.nlm.nih.gov webcite.This article was reviewed by Arcady Mushegian, Nick V. Grishin, and Frank Eisenhaber.
%U http://www.biology-direct.com/content/7/1/12/abstract