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Improved tools for biological sequence comparison.

W R Pearson1, D J Lipman

  • 1Department of Biochemistry, University of Virginia, Charlottesville 22908.

Proceedings of the National Academy of Sciences of the United States of America
|April 1, 1988
PubMed
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We developed FASTA, FASTP, and LFASTA computer programs for efficient protein and DNA sequence comparison. These tools enhance database searching, similarity score evaluation, and identification of local sequence similarities.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate comparison of protein and DNA sequences is crucial for understanding biological function and evolution.
  • Existing sequence analysis tools may lack sensitivity or comprehensive features for identifying local similarities.

Purpose of the Study:

  • To introduce three novel computer programs (FASTA, RDF2, LFASTA) for advanced sequence comparison.
  • To enhance the capabilities for searching sequence databases and evaluating similarity scores.
  • To facilitate the identification of periodic structures and local sequence similarities.

Main Methods:

  • Development of the FASTA program, a sensitive derivative of FASTP, incorporating an additional step for joining multiple similarity regions.
  • Implementation of the RDF2 program for assessing similarity score significance using a shuffling method.

Related Experiment Videos

  • Design of the LFASTA program for visualizing local sequence similarities through graphic matrix plots or individual alignments.
  • Generalization of the programs to support various scoring matrices for DNA and protein sequence comparisons.

    • Main Results:

    • FASTA demonstrates increased sensitivity in detecting related sequences compared to FASTP.
    • RDF2 provides a robust method for evaluating the statistical significance of sequence similarity scores.
    • LFASTA effectively visualizes and quantifies local sequence similarities between two sequences.
    • The developed programs offer flexibility in analyzing both protein and DNA sequences using diverse scoring systems.

    Conclusions:

    • The FASTA, RDF2, and LFASTA programs represent significant advancements in sequence analysis tools.
    • These programs improve the accuracy and scope of sequence database searching and similarity assessment.
    • The ability to identify and visualize local similarities aids in the discovery of functional relationships and evolutionary patterns.