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Related Experiment Videos

Serial BLAST searching.

Ian Korf1

  • 1The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK. ik1@sanger.ac.uk

Bioinformatics (Oxford, England)
|August 13, 2003
PubMed
Summary
This summary is machine-generated.

Serial BLAST searches enhance speed and sensitivity in sequence analysis. This method uses a fast, insensitive search to pre-screen databases, followed by a slow, sensitive search for accurate alignments, overcoming computational bottlenecks.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Translating BLAST algorithms identify protein-coding genes by detecting amino acid similarities in nucleotide sequences.
  • These searches are computationally intensive, often causing bottlenecks in sequence analysis.
  • Optimizing parameters for speed can compromise the detection of low-scoring alignments.

Purpose of the Study:

  • To improve the speed and sensitivity of sequence analysis pipelines.
  • To address the computational intensity of BLAST searches.
  • To develop a strategy that minimizes the loss of low-scoring alignments.

Main Methods:

  • Implemented a serial search strategy using BLAST.
  • Utilized a fast, insensitive search for initial database pre-screening.

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  • Employed a slow, sensitive search for detailed sequence alignment generation.

    • Main Results:

    • Serial BLAST searches demonstrated significant improvements in both speed and sensitivity.
    • The pre-screening approach effectively reduced the computational load.
    • High-scoring alignments remained detectable despite parameter tuning for speed.

    Conclusions:

    • The serial search strategy offers a viable solution to accelerate sequence analysis.
    • This method balances computational efficiency with the preservation of alignment sensitivity.
    • Serial BLAST searches are a powerful tool for overcoming bottlenecks in bioinformatics pipelines.