ToxProt25: Analysis of ToxProt (2017-2025)

Comparative analysis of toxin proteins from ToxProt between UniProtKB 2017 and 2025 releases.

🎯 Project Overview

This project analyzes changes in toxin-related proteins across two UniProtKB snapshots (2017 and 2025):

• Taxonomic changes: Species representation and new taxa emergence
• Habitat patterns: Marine vs terrestrial protein family distributions
• Protein families: Classification and abundance changes
• GO-term analysis: Functional annotation comparisons
• PTM analysis: Post-translational modification patterns
• Curation insights: Protein family renamings and annotation improvements
• Protein space: 2D embedding visualization using ProtSpace

🚀 Quick Start

Prerequisites

• Python 3.12+
• UV package manager (recommended) or pip

Installation

# Clone the repository
git clone <repository-url>
cd toxprot25

# Install dependencies with UV (recommended)
uv sync

# OR install with pip
pip install -e .

🔬 Key Analyses

1. Data Processing

Step 1: Parse SwissProt DAT files (src/data_processing/parse_sprot_dat.py)

Extracts entries matching: (taxonomy_id:33208) AND ((cc_tissue_specificity:venom) OR (keyword:KW-0800))

Key features:

• Process signal peptides for mature protein sequences
• Extract protein metadata (names, families, length, mass)
• Capture functional annotations (tissue specificity, toxic dose)
• Extract post-translational modifications (MOD_RES, CARBOHYD, DISULFID, CROSSLNK, LIPID)
• Auto-download PTM controlled vocabulary (ptmlist.txt)

Step 2: Clean and enrich data (src/data_processing/clean_data.py)

• Standardize protein family names
• Create FASTA files with signal peptide removal
• Add taxonomic information (phylum, class, order, family, genus, species)
• Add habitat classification (marine/terrestrial)

Step 3: Remove fragments (src/data_processing/remove_fragments.py)

• Filter out fragment sequences for specific analyses

2. Comparative Analyses (2017 vs 2025)

Protein Families (src/analysis/analyze_protein_families.py)

• Distribution comparisons with stacked bar charts
• Sequence length histograms
• Summary statistics tables

Taxonomic Changes (src/analysis/analyze_taxa.py)

• Top taxa distribution comparison
• Newcomer orders and families identification
• Species-level counting

Habitat Patterns (src/analysis/analyze_habitat.py)

• Marine vs terrestrial protein family distribution
• Percentage and absolute changes
• Dual-habitat family analysis
• Venn diagrams and heatmaps

Post-Translational Modifications (src/analysis/analyze_ptm.py)

• PTM type distributions
• Modification count analysis
• Comparative statistics

GO Terms (src/analysis/analyze_go_terms.py)

• Functional annotation comparisons
• GO term enrichment changes

Curation Tracking (src/analysis/generate_family_renaming_report.py)

• Protein family name changes tracking
• Systematic renaming identification

Protein Evidence (src/analysis/plot_protein_evidence_sankey.py)

• Sankey diagrams showing protein evidence flow

📝 Data Sources

• UniProtKB/SwissProt: Nov 2017 (201711_sprot.dat) and Jan 2025 (202501_sprot.dat)
• Habitat classification: Manual curation from taxonomic families