This repository contains Python scripts developed for the MSc Bioinformatics assignment on variant identification and annotation in candidate genes related to Tetralogy of Fallot. The scripts automate extraction of coding sequences (CDS), pairwise comparison of cDNA variants against reference transcripts, and annotation of coding changes in HGVS format.
- Python: Version 3.8 or higher
- Packages:
Extracts the coding sequence (CDS) region from a provided mRNA FASTA file using RefSeq coordinates.
Input: mRNA FASTA file
Output: Trimmed CDS FASTA (*_CDS.fa)
Main libraries: Bio.SeqIO, os
Compares two nucleotide sequences, identifies aminoo acid change amd outputs information in HGVS format.
Input: two mRNA FASTA files Output: Terminal information on the amino acid change in HGVS notation