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Related Experiment Videos

Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm.

K Y Cockwell1, I G Giles

  • 1Department of Biochemistry, School of Biochemical and Physiological Sciences, University of Southampton, UK.

Computer Applications in the Biosciences : CABIOS
|July 1, 1989
PubMed
Summary
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Two new programs, MOTIF and PATTERN, efficiently scan biological sequences for user-defined motifs and patterns. They offer flexible input options and automatically detect sequence formats, aiding in data analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Sequence Analysis

Background:

  • Motif discovery is crucial for understanding biological sequences.
  • Existing tools may lack flexibility in defining and searching patterns.
  • Automated format detection simplifies sequence data handling.

Purpose of the Study:

  • To introduce MOTIF and PATTERN, software tools for sequence analysis.
  • To enable users to define and search for sequence motifs and patterns.
  • To provide automated sequence format detection.

Main Methods:

  • Development of MOTIF and PATTERN software.
  • Implementation of a user-friendly notation for motif definition.
  • Integration of identity and set membership criteria for pattern matching.

Related Experiment Videos

  • Inclusion of an algorithm for automatic detection of six sequence file formats.

    • Main Results:

    • MOTIF and PATTERN successfully scan sequences for defined motifs and patterns.
    • The programs support interactive and batch processing modes.
    • The automated format detection algorithm reliably identifies sequence entry formats.

    Conclusions:

    • MOTIF and PATTERN provide efficient and flexible tools for sequence motif and pattern analysis.
    • The software simplifies data preprocessing through automatic format detection.
    • These programs enhance the capabilities of bioinformatics sequence analysis workflows.