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Syntactic sugars: crafting a regular expression framework for glycan structures.

Alexander R Bennett1, Daniel Bojar2,3

  • 1Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 41390 Gothenburg, Sweden.

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|May 6, 2024
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Summary
This summary is machine-generated.

We developed a novel regular expression system for analyzing complex glycan structures, enabling automated motif annotation and differential expression analysis for N-glycans. This tool simplifies computational glycomics research.

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Area of Science:

  • Glycobiology
  • Computational Biology
  • Bioinformatics

Background:

  • Structural analysis of glycans is challenging due to complex sequences.
  • Automating analysis of specific glycan features, like N-glycan branches, is difficult.

Purpose of the Study:

  • Introduce a novel regular expression system for glycan analysis.
  • Enable automated annotation and analysis of complex glycan motifs.
  • Facilitate research into glycan sequence content and function.

Main Methods:

  • Developed a feature-complete regular expression system tailored for glycans.
  • Aligned the system with standard regular expression formatting.
  • Implemented the framework within the open-source glycowork package (version 1.1+).

Main Results:

  • The system allows for annotation of glycan motifs of arbitrary complexity.
  • Enables automated differential expression analysis on specific glycan sequences.
  • Facilitates elucidation of branch-specific lectin binding specificities.

Conclusions:

  • Glycan regular expressions empower computational analyses of complex glycan sequences.
  • The developed framework enhances automation in glycomics research.
  • The tool is accessible via the open-source glycowork package.