Example script demonstrating the use of BioPython to compare genomic sequences at a given gene location.

Abstraction: BioPython script comparing sample sequences to reference genome for SNP detection

Key points:

• Uses BioPython SeqIO.index() to load reference (SGD S288C R64-1-1 FASTA) and sample FASTQ files for per-gene comparison
• Handles Crick strand genes by applying reverse_complement() when start > end coordinates
• Detects SNPs by comparing reference and sample base-by-base; reports location, 10-base context, and total count
• If fewer than 5 SNPs found, prints detailed positional report; always reports count and fraction differing
• Gene coordinates hardcoded as dict: HIS3=(chr15, 721946, 722608), BRR1=(chr16, 672471, 673496)
• Chromosome IDs sorted alphabetically from SGD reference and mapped to numeric order

Connections: Biopython · Github · Bioinformatics · Sequence Analysis · Snp Analysis

Source: https://gist.github.com/CnrLwlss/5935118