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Logo of bioldirectBioMed CentralBiomed Central Web Sitesearchsubmit a manuscriptregisterthis articleBiology DirectJournal Front Page
 
Biol Direct. 2012; 7: 12.
Published online Apr 17, 2012. doi:  10.1186/1745-6150-7-12
PMCID: PMC3438057
Domain enhanced lookup time accelerated BLAST
Grzegorz M Boratyn,corresponding author1 Alejandro A Schäffer,1 Richa Agarwala,1 Stephen F Altschul,1 David J Lipman,1 and Thomas L Madden1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD, 20894, USA
corresponding authorCorresponding author.
Grzegorz M Boratyn: boratyng/at/ncbi.nlm.nih.gov; Alejandro A Schäffer: schaffer/at/helix.nih.gov; Richa Agarwala: richa/at/helix.nih.gov; Stephen F Altschul: altschul/at/ncbi.nlm.nih.gov; David J Lipman: lipman/at/ncbi.nlm.nih.gov; Thomas L Madden: madden/at/ncbi.nlm.nih.gov
Received December 16, 2011; Accepted April 17, 2012.
Abstract
Background
BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific score matrix (PSSM) for searching the database in round i + 1. Biegert and Söding developed Context-sensitive BLAST (CS-BLAST), which combines information from searching the sequence database with information derived from a library of short protein profiles to achieve better homology detection than PSI-BLAST, which builds its PSSMs from scratch.
Results
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.
Conclusions
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.
Reviewers
This article was reviewed by Arcady Mushegian, Nick V. Grishin, and Frank Eisenhaber.
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