Domain enhanced lookup time accelerated BLAST

Biol Direct. 2012 Apr 17;7:12. doi: 10.1186/1745-6150-7-12.

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.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Algorithms
  • Computational Biology / methods
  • Databases, Protein*
  • Internet
  • Protein Structure, Tertiary*
  • ROC Curve
  • Reproducibility of Results
  • Search Engine / methods*
  • Sensitivity and Specificity
  • Sequence Alignment / methods
  • Sequence Analysis, Protein / methods
  • Sequence Homology, Amino Acid
  • Software*
  • Time Factors