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Basic local alignment search tool.

S F Altschul1, W Gish, W Miller

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.

Journal of Molecular Biology
|October 5, 1990
PubMed
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A new rapid sequence comparison method, Basic Local Alignment Search Tool (BLAST), approximates maximal segment pair scores for efficient database searches. This tool offers significant speed and flexibility for DNA and protein sequence analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional sequence comparison methods can be computationally intensive.
  • There is a need for faster and more sensitive tools for analyzing biological sequences.
  • Understanding local sequence similarity is crucial in various biological contexts.

Purpose of the Study:

  • To introduce a novel approach for rapid sequence comparison.
  • To present the Basic Local Alignment Search Tool (BLAST) algorithm.
  • To analyze the performance and statistical significance of BLAST alignments.

Main Methods:

  • BLAST approximates alignments optimizing the Maximal Segment Pair (MSP) score.
  • Utilizes mathematical results on stochastic properties of MSP scores for analysis.

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  • The algorithm is designed for simplicity, robustness, and implementational flexibility.

    • Main Results:

    • BLAST achieves high sensitivity in sequence comparisons.
    • The method is significantly faster (an order of magnitude) than existing tools.
    • Enables statistical assessment of alignment significance.

    Conclusions:

    • BLAST provides a flexible and mathematically tractable solution for sequence analysis.
    • Applicable to diverse tasks including database searches, motif identification, and gene finding.
    • Represents a substantial advancement in rapid and sensitive biological sequence comparison.