CodeClub1 Program1

This program extracts the vif gene sequences from a set of HIV sequences by aligning them to the HXB2 reference genome.

What it does

• Reads the HXB2 reference sequence from data/hxb2.fasta
• Reads multiple query sequences from data/sequences.fasta
• For each query sequence:
  • Performs a global alignment against HXB2
  • Maps the vif gene coordinates (positions 5243-5619 in HXB2) to the query sequence
  • Extracts and prints the corresponding vif sequence in FASTA format

How to run

1. Ensure you have uv installed.

2. Navigate to the project root directory.

3. Run the program:

   uv run program1

The output will be printed to stdout, with each vif sequence in FASTA format.

Output format

For each input sequence, the program outputs:

• A FASTA header: >{sequence_id}_vif
• The extracted vif sequence

Notes

• The program uses global pairwise alignment with BioPython's PairwiseAligner.
• Coordinate mapping is handled by the aligntools library.
• The program skips sequences where the vif region cannot be successfully mapped.