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A large database DNA sequence handling program with generalized searching specifications

P A Stockwell

    Nucleic Acids Research
    |January 11, 1982
    PubMed
    Summary
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    This program efficiently manages large DNA sequence files using a paging system to minimize memory usage. It includes user-friendly features and a flexible code for base group specifications, enhancing DNA data analysis.

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomic Data Management

    Background:

    • Managing large DNA sequence data presents challenges in terms of computational resources.
    • Existing tools may have limitations in handling extensive genomic datasets efficiently.

    Purpose of the Study:

    • To develop a software program for the creation and manipulation of very long DNA sequence files.
    • To address memory constraints associated with large-scale sequence data processing.
    • To introduce a flexible coding system for generalized base specifications.

    Main Methods:

    • Implementation of a proprietary paging system to load sequence segments into a small internal buffer.
    • Development of a user-friendly menu-driven interface with error-handling capabilities.

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  • Inclusion of a generalized base specification code for sequence files and search parameters.

    • Main Results:

    • The program effectively handles DNA sequence data of significant lengths without excessive memory requirements.
    • A novel code for generalized base specifications (e.g., Purines, Pyrimidines) was successfully devised and implemented.
    • Optimized versions were created for specific operating systems, including DIGITAL's RT11 and FORTRAN VI environments.

    Conclusions:

    • The developed program provides an efficient and accessible solution for managing and analyzing large DNA sequence datasets.
    • The paging system and generalized base code enhance the utility and flexibility of the software for bioinformatics applications.
    • The program's adaptability to different operating systems ensures broad applicability in genomic research.