GlycoSiteAlign

GlycoSiteAlign aligns amino acid sequences surrounding glycosylation sites according to glycan structural features to identify amino acid patterns linked to glycan–protein interactions.

Key Features:

• Alignment based on glycan structure: Aligns sequences by selected glycan features such as fucosylated versus non-fucosylated to compare the local amino acid environment.
• Database integration: Leverages UniCarbKB and UniProtKB data (hosted on ExPASy) for glycan and protein annotations used in alignments.
• Customizable sequence fragment length: Allows variable selection of protein fragment lengths around glycosylation sites to tailor the alignment window.
• Inclusion of homologous proteins: Optionally includes 90% homologous proteins in alignments to assess evolutionary conservation.

Scientific Applications:

• Amino acid pattern discovery: Identifies characteristic amino acid motifs associated with specific glycan features.
• Glycan–site constraint analysis: Reveals constraints linking particular glycan structures to their glycosylation sites.
• Predictive model refinement: Provides empirical patterns to refine and validate glycosylation prediction models.

Methodology:

Aligns amino acid sequences surrounding glycosylation sites with variable window lengths based on user-selected glycan features (e.g., fucosylated vs non-fucosylated) and integrates UniCarbKB and UniProtKB data (hosted on ExPASy); the database is updated as new data become available.