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Related Experiment Videos

Sequence search on a supercomputer.

O Gotoh, Y Tagashira

    Nucleic Acids Research
    |January 10, 1986
    PubMed
    Summary
    This summary is machine-generated.

    Researchers developed optimized software for rapid searching of nucleic acid and protein sequence databases. This computational tool significantly accelerates sequence similarity analysis on supercomputers.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • High-throughput sequencing generates vast amounts of biological data.
    • Efficient searching of sequence databases is crucial for biological discovery.
    • Existing methods can be computationally intensive for large datasets.

    Purpose of the Study:

    • To develop and optimize computational programs for searching nucleic acid and protein sequence databases.
    • To enhance the speed and efficiency of sequence similarity searches.
    • To leverage supercomputing resources for accelerated biological data analysis.

    Main Methods:

    • Programs developed in FORTRAN 77.
    • Optimization for vector processing on a Hitachi S810-20 supercomputer.

    Related Experiment Videos

  • Utilized Protein Identification Resource (PIR) and GenBank sequence databases.

    • Main Results:

    • A 500-residue protein sequence search against the PIR database (0.5M residues) completed in 45 seconds.
    • An exhaustive search of a 1500-base nucleotide sequence against mammalian sequences in GenBank (1.2M bases) took approximately 4 minutes.
    • A faster version of the software reduced CPU time by approximately 75%.

    Conclusions:

    • The developed programs offer a significant speed improvement for sequence database searching.
    • Optimized software enables rapid identification of similar sequences within large biological datasets.
    • Supercomputer-based sequence analysis is a viable approach for accelerating bioinformatics research.