glycobiology

Glycobiology: Glycosylation Analysis

Overview

Glycobiology provides lightweight computational tools for predicting and analyzing glycosylation sites in protein sequences. This skill covers N-glycosylation sequon motif finding (N-X-S/T where X is not P), O-glycosylation hotspot prediction using a sliding window serine/threonine density heuristic, glycan structure tool references, and combined glycoprotein analysis with domain mapping. All analyses use pure Python with minimal dependencies (Biopython for sequence I/O, regex for pattern matching).

When to Use This Skill

• Predicting N-glycosylation sites from protein sequences
• Identifying O-glycosylation hotspot regions
• Planning glycosylation site mutagenesis experiments
• Comparing predicted vs experimentally determined glycosylation sites
• Annotating glycosylation in biotherapeutic protein design
• Surveying glycan analysis tools for downstream structural studies

Related Skills: For protein function and existing glycosylation annotations use uniprot-database. For protein 3D structure and site accessibility use alphafold-database. For sequence manipulation use biopython.

Installation

uv pip install biopython numpy

No additional dependencies required — this skill uses pure Python.

Quick Start

import re

def find_n_glycosylation_sites(sequence):
    """Find N-X-S/T sequons where X != P."""
    sites = []
    for i in range(len(sequence) - 2):
        if sequence[i] == 'N' and sequence[i+1] != 'P' and sequence[i+2] in ('S', 'T'):
            sites.append({
                'position': i + 1,  # 1-based
                'motif': sequence[i:i+3],
                'context': sequence[max(0,i-3):i+6]
            })
    return sites

# Example: human EPO
epo_seq = "MGVHECPAWLWLLLSLLSLPLGLPVLGAPPRLICDSRVLERYLLEAKEAENITTGCAEHCSLNENITVPDTKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVNSSQPWEPLQLHVDKAVSGLRSLTTLLRALGAQKEAISPPDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDR"

sites = find_n_glycosylation_sites(epo_seq)
print(f"N-glycosylation sites: {len(sites)}")
for s in sites:
    print(f"  Position {s['position']}: {s['motif']} (context: ...{s['context']}...)")