eli766/pseudomonas-phage-genomics

Comparative genomic analysis of Pseudomonas aeruginosa phages isolated in Africa # Pseudomonas Phage Comparative Genomics ## 🎯 Project Overview Comparative genomic analysis of *Pseudomonas aeruginosa* phages isolated in Africa to identify genomic features enabling effective combat against multidrug-resistant (MDR) strains. ## 🎯 Objectives 1. **Genome Analysis**: Retrieve and compare whole genome sequences from African *P. aeruginosa* phages 2. **Protein Characterization**: Perform in silico analysis of tail fiber and tail spike proteins 3. **Host Range Prediction**: Predict host specificity based on structural and functional features ## 📁 Project Structure # Pseudomonas Phage Comparative Genomics ## 🎯 Project Overview Comparative genomic analysis of *Pseudomonas aeruginosa* phages isolated in Africa to identify genomic features enabling effective combat against multidrug-resistant (MDR) strains. ## 🎯 Objectives 1. **Genome Analysis**: Retrieve and compare whole genome sequences from African *P. aeruginosa* phages 2. **Protein Characterization**: Perform in silico analysis of tail fiber and tail spike proteins 3. **Host Range Prediction**: Predict host specificity based on structural and functional features ## 📁 Project Structurepseudomonas-phage-genomics/ ├── data/ │ ├── raw/ # Original genome sequences │ ├── processed/ # Cleaned and formatted data │ ├── reference/ # Reference genomes and annotations │ └── metadata/ # Sample information and metadata ├── scripts/ │ ├── 01_data_retrieval/ # Genome download scripts │ ├── 02_annotation/ # Pharokka and annotation tools │ ├── 03_comparative/ # Roary, MAFFT, phylogeny │ └── 04_visualization/ # Plotting and figure generation ├── notebooks/ │ ├── 01-data-retrieval.ipynb │ ├── 02-genome-annotation.ipynb │ ├── 03-comparative-analysis.ipynb │ └── 04-host-prediction.ipynb ├── results/ │ ├── figures/ # Publication-ready figures │ ├── tables/ # Summary ta …