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PALM--a pattern language for molecular biology

C Helgesen1, P R Sibbald

  • 1Department of Informatics, University of Bergen, Norway.

Proceedings. International Conference on Intelligent Systems for Molecular Biology
|January 1, 1993
PubMed
Summary
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Researchers developed the Pattern Analysis Language for Molecular biology (PALM) to describe complex patterns in biological sequences. This declarative language offers high expressive power for defining various sequence patterns, including approximate ones.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Describing patterns in molecular biology sequences is crucial for understanding biological functions.
  • Existing methods may lack the expressiveness or clarity needed for complex pattern representation.

Purpose of the Study:

  • Introduce a novel pattern language, PALM (Pattern Analysis Language for Molecular biology).
  • Provide a declarative, clear, and concise method for representing knowledge about molecular biology sequence patterns.

Main Methods:

  • Developed a new formal language, PALM.
  • Demonstrated its expressive power through theoretical analysis and examples.
  • Incorporated features like parameter attachment, variables, and procedural attachment.

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Main Results:

  • PALM can define any regular or context-free language, and higher languages in the Chomsky hierarchy.
  • The language supports the definition of approximate patterns.
  • Rigorous definition and illustrative examples showcase PALM's capabilities.

Conclusions:

  • PALM offers a powerful and flexible tool for representing diverse molecular biology sequence patterns.
  • Its declarative nature enhances clarity and conciseness in knowledge representation.
  • The language's expressiveness extends to complex pattern definitions, including approximate matching.