Source: https://github.com/aipoch/medical-research-skills

biopython-alignment

When to Use

• You need global alignment between two protein (or nucleotide) sequences and want a reproducible score and aligned strings.
• You need local alignment to find the best matching fragment/subsequence between two DNA/RNA/protein sequences.
• You need to read, write, or convert multiple sequence alignment (MSA) files (e.g., FASTA/Clustal/Stockholm) using Biopython I/O.
• You want to compute alignment statistics (e.g., identity, coverage, conservation per column) and filter alignments by thresholds.
• You need to apply substitution matrices (e.g., BLOSUM62) and tune gap penalties for biologically meaningful scoring.

Key Features

• Pairwise alignment via Bio.Align.PairwiseAligner (global and local modes).
• Alignment scoring with configurable match/mismatch and gap penalties.
• Protein substitution matrices via Bio.Align.substitution_matrices (e.g., BLOSUM/PAM).
• MSA parsing and serialization via Bio.AlignIO (read/write/format conversion).
• Basic alignment statistics: identity, aligned length, coverage, and MSA column conservation.