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Related Experiment Video

Updated: May 23, 2026

Blast Quantification Using Hopkinson Pressure Bars
09:41

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Published on: July 5, 2016

Domain enhanced lookup time accelerated BLAST.

Grzegorz M Boratyn1, Alejandro A Schäffer, Richa Agarwala

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA. boratyng@ncbi.nlm.nih.gov

Biology Direct
|April 19, 2012
PubMed
Summary
This summary is machine-generated.

Domain Enhanced Lookup Time Accelerated BLAST (DELTA-BLAST) improves remote protein homology detection by searching pre-constructed position-specific score matrices (PSSMs) before sequence databases. This method offers superior performance compared to existing tools like CS-BLAST.

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Last Updated: May 23, 2026

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Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

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Published on: April 23, 2011

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • BLAST is a standard tool for sequence comparison, particularly in protein analysis.
  • Position-Specific Iterated BLAST (PSI-BLAST) uses iterative database searching to build position-specific score matrices (PSSMs).
  • Context-Sensitive BLAST (CS-BLAST) enhances homology detection by integrating sequence database searches with protein profile libraries.

Purpose of the Study:

  • Introduce DELTA-BLAST, a novel method for enhanced protein homology detection.
  • Improve upon the performance of existing BLAST variants like PSI-BLAST and CS-BLAST.

Main Methods:

  • DELTA-BLAST utilizes a pre-constructed library of PSSMs from the NCBI Conserved Domain Database (CDD).
  • It performs an initial search against this PSSM database before querying the main protein sequence database.
  • The method aims to accelerate homology detection and improve sensitivity.

Main Results:

  • DELTA-BLAST demonstrates superior homology detection compared to CS-BLAST, achieving a ROC5000 of 0.270 versus 0.116 in initial searches.
  • While the performance gap narrows in iterated searches, DELTA-BLAST consistently outperforms CS-BLAST.
  • The use of pre-constructed PSSMs significantly enhances detection capabilities.

Conclusions:

  • DELTA-BLAST is an effective tool for identifying remote protein homologs.
  • The program is accessible via the "Protein BLAST" link on the NCBI BLAST website.