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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
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Database indexing for production MegaBLAST searches.

Aleksandr Morgulis1, George Coulouris, Yan Raytselis

  • 1Department of Health and Human Services, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA.

Bioinformatics (Oxford, England)
|June 24, 2008
PubMed
Summary

Indexed MegaBLAST speeds up sequence homology searches by preprocessing databases, offering significant performance improvements over non-indexed versions. This enhanced BLAST module is now faster and more efficient for practical bioinformatics applications.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional BLAST preprocesses query sequences, limiting homology search speed.
  • Previous database-preprocessing methods were restricted to highly similar sequence matches.
  • Research suggested database preprocessing could enhance performance.

Purpose of the Study:

  • To develop and evaluate an indexed version of MegaBLAST for faster sequence homology searches.
  • To improve the performance of BLAST by preprocessing the database.
  • To enhance the NCBI Web BLAST service's query response times.

Main Methods:

  • Developed an indexed MegaBLAST module for searching a database index.
  • Created the makembindex program to preprocess databases for rapid seed searching.
  • Modified NCBI's Web BLAST service for dedicated database machines and optimized queueing.

Main Results:

  • Indexed MegaBLAST demonstrated faster performance than the non-indexed version in most practical scenarios.
  • Indexed MegaBLAST outperformed miBLAST in tests with 200 queries.
  • Optimized NCBI's Web BLAST service, resulting in reduced query response times.

Conclusions:

  • Indexed MegaBLAST offers a significant performance improvement for sequence homology searches.
  • The makembindex tool and indexed MegaBLAST are available as part of the NCBI C++ toolkit.
  • Indexed MegaBLAST has been successfully deployed in production on NCBI's Web BLAST service.