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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
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GlycoSiteAlign: Glycosite Alignment Based on Glycan Structure.

Alessandra Gastaldello1,2, Davide Alocci1,2, Jean-Luc Baeriswyl1,3

  • 1Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , 7 route de Drize, 1227 Geneva, Switzerland.

Journal of Proteome Research
|August 16, 2016
PubMed
Summary
This summary is machine-generated.

GlycoSiteAlign aligns protein sequences around glycosylation sites based on glycan structure. This tool helps identify amino acid patterns linked to specific glycan-protein interactions, advancing glycomics research.

Keywords:
amino acid patternsglycan structureglycoproteinglycositeglycosylationsequence alignment

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Glycomics

Background:

  • Glycosylation is a crucial post-translational modification.
  • Understanding glycan-protein interactions is vital for biological processes.
  • Predicting glycosylation sites and associated glycans remains challenging.

Purpose of the Study:

  • To introduce GlycoSiteAlign, a novel bioinformatics tool.
  • To facilitate the identification of amino acid sequence patterns associated with specific glycan structures.
  • To explore the relationship between glycan features and their surrounding protein sequences.

Main Methods:

  • GlycoSiteAlign utilizes data from UniCarbKB and UniProtKB databases.
  • The tool aligns variable-length amino acid sequences around glycosylation sites.
  • Users can specify glycan features and protein fragment length, with options for homology inclusion.

Main Results:

  • The tool generates alignments revealing potential amino acid patterns linked to specific glycan features (e.g., fucosylation).
  • Alignments can be previewed and downloaded for further analysis.
  • GlycoSiteAlign provides insights into glycan-specific sequence constraints.

Conclusions:

  • GlycoSiteAlign is a valuable exploratory resource for glycomics research.
  • It aids in assessing and refining knowledge of glycan-structure-glycosite linkages.
  • The tool has the potential to improve future glycosylation prediction models.