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Object-oriented sequence analysis: SCL--a C++ class library

W Vahrson1, K Hermann, J Kleffe

  • 1Abteilung Molekularbiologie und BioInformatik, Freie Universitä Berlin, Germany. wova@zedat.fu-berlin.de

Computer Applications in the Biosciences : CABIOS
|April 1, 1996
PubMed
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The Sequence Class Library (SCL) offers C++ classes for DNA and protein sequence analysis. It supports database access, sequence alignment, and general programming tasks, promoting flexible algorithm development.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Software Engineering

Background:

  • Sequence analysis is crucial in molecular biology.
  • Object-oriented programming offers advantages for complex data structures and algorithms.
  • Existing libraries may lack flexibility or comprehensive features for sequence analysis.

Purpose of the Study:

  • To introduce the Sequence Class Library (SCL), a C++ library for sequence analysis.
  • To provide a flexible and comprehensive set of tools for bioinformatics tasks.
  • To facilitate explorative programming and algorithm experimentation.

Main Methods:

  • Developed SCL using object-oriented programming principles in C++.
  • Designed flexible sequence classes, database access classes, and collection management classes.

Related Experiment Videos

  • Included classes for higher-level tasks like sequence alignment and general programming utilities.

    • Main Results:

    • SCL provides a robust framework for analyzing DNA and protein sequences.
    • The library includes components for database interaction, sequence manipulation, and alignment.
    • General programming support classes enhance usability and error handling.

    Conclusions:

    • SCL enables efficient and flexible development of bioinformatics applications.
    • The library encourages an explorative programming style for algorithm development.
    • SCL serves as a valuable tool for researchers in computational biology and bioinformatics.