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Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence

B Billoud1, M Kontic, A Viari

  • 1Atelier de Bio-informatique URA CNRS 448, Institut Curie, Paris, France.

Nucleic Acids Research
|April 15, 1996
PubMed
Summary

This study introduces Palingol, a novel programming language for biological sequence and structure searching. Palingol simplifies the identification of DNA/RNA structures by separating search criteria from search execution.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Biological signals at the DNA/RNA level depend on both sequence and spatial structure.
  • Existing search programs often intertwine biological definition with computational implementation, making them complex and time-consuming.
  • General-purpose programming languages are not ideally suited for simultaneous sequence and structure searching.

Purpose of the Study:

  • To develop a general-purpose search program for DNA/RNA sequences that considers both structural and sequential motifs.
  • To introduce a novel programming language, Palingol, for manipulating and searching complex biological structures.
  • To simplify the process of defining and searching for specific structural constraints in biological databases.

Main Methods:

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  • Development of a general representation for biological structures suitable for database scanning.
  • Design and implementation of the Palingol programming language with specific data types for structural elements like helices.
  • Utilizing a declarative approach in Palingol where users specify search targets ('what') and the engine handles the search mechanism ('how').

Main Results:

  • Palingol enables the manipulation of structural elements (e.g., helices) into complex arrangements.
  • The declarative nature of Palingol simplifies the creation of scanning programs.
  • Structural constraints for biological searches are more clearly identified and managed.

Conclusions:

  • Palingol offers a more efficient and user-friendly approach to searching biological databases for sequence-structure combinations.
  • The language facilitates a clearer definition of search criteria, improving the identification of biological signals.
  • This work advances the field of bioinformatics by providing a specialized tool for structure-based sequence analysis.