Domain enhanced lookup time accelerated BLAST

doi:10.1186/1745-6150-7-12

Biol Direct. 2012; 7: 12.

Published online 2012 April 17. doi: 10.1186/1745-6150-7-12

PMCID: PMC3438057

Domain enhanced lookup time accelerated BLAST

Grzegorz M Boratyn,¹ 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 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.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article has been cited by other articles in PMC.

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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