This repository contains the Python code and associated files used for analyzing the conservation of homeobox genes across various non-primate species compared to Homo sapiens. The research aims to answer the question: "How similar are homeobox genes in various non-primates to those in Homo sapiens, and which species show the most significant levels of conservation?"
- Sequence alignment done via Biopython pairwise aligner
- Percent identity calculation
- Data extraction from the Ensembl database
- CSV output containing percent identity scores for each gene
- CSV output for each Homeobox gene class
- Sequences prealigned for Homeobox genes coding sequences (Pseudogenes not included)
- Python 3.9
- Biopython
- pandas
- NumPy
- Using console clone the repository
git clone https://github.com/LauriSarap/GeneComparisonTool.git
- Navigate to the repository folder
cd GeneComparisonTool
- Install the required Python packages
pip install biopython
pip install pandas
- Run the main python script
cd src
python main.py
main.py: The main Python script for running the analysis.src/data/: Folder containing the raw FASTA files and where .csv files are createdsrc/cache/: Folder where alignments are cached
- The code is tailored to work with pre-computed potential orthologous genes from the Ensembl database.
- The current scoring system for sequence alignment is basic, giving a score of +1 for a match and 0 for a mismatch.
This research was conducted using data from reputable sources, such as the HUGO Gene Nomenclature Committee (HGNC) and Ensembl databases.
This project is licensed under the MIT License - see the LICENSE.md file for details.