This project investigates evolutionary and structural features of Plasmodium falciparum proteins using sequence alignment, conservation analysis, and phylogenetic trees. It was developed as part of the Proteomes, Interactomes, and Biological Networks course (AA 2024–2025) at the University of Bologna.
| Notebook | Description |
|---|---|
conserved_regions.ipynb |
Builds a phylogenetic tree using IQ-TREE and analyzes conserved regions. Includes plots of the results. |
matrices.ipynb |
Creates distance matrices and analyses cluster |
tree_v2.ipynb |
An alternative version of the phylogenetic tree visualization using IQ-TREE; optimized for 4-strain plots. |
preliminary_analysis.ipynb |
Initial data exploration and preprocessing of Plasmodium falciparum protein sequences. |
- IQ-TREE: For constructing phylogenetic trees from aligned sequences.
- Python: Data manipulation, visualization, and matrix generation.
You can open any notebook directly in Google Colab:
This work is part of a final team project requiring use of at least 4 resources, formats, or tools such as:
- PDB, UniProt, Ensembl
- FASTA, PDB, DSSP formats
- ChimeraX, PyMOL, Cytoscape, NetworkX