Individual skill

biopython-alignment

Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.

scientific-skills/Data Analysis/biopython-alignment/SKILL.md

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bioinformatics Repository topic
computational-biology Repository topic
data-analysis Repository topic
ai Repository topic
biology Repository topic
cancer-genomics Repository topic
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genomics Repository topic
medical Repository topic
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> **Source**: [https://github.com/aipoch/medical-research-skills](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).