AlterLab Biopython Bioinformatics Skill
Skill Verified ActiveComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. Part of the AlterLab Academic Skills suite.
To serve as a powerful, programmatic toolkit for a wide range of computational molecular biology tasks, suitable for batch processing and custom bioinformatics pipelines.
Features
- Sequence manipulation and analysis
- Parsing of biological file formats (FASTA, GenBank, PDB)
- Programmatic access to NCBI databases (Entrez)
- BLAST search automation and result parsing
- Phylogenetic tree analysis
- Structural bioinformatics analysis
Use Cases
- Working with biological sequences (DNA, RNA, protein)
- Reading, writing, or converting biological file formats
- Accessing and querying NCBI databases
- Performing BLAST searches or analyzing results
- Analyzing protein structures and phylogenetic trees
Non-Goals
- Replacing dedicated GUI tools for quick lookups (e.g., gget)
- Providing multi-service integration beyond Biopython's scope (suggests bioservices)
- Serving as a general-purpose programming assistant
Practices
- Sequence handling
- Database access
- Sequence alignment
- Phylogenetics
- Structural bioinformatics
Prerequisites
- Python 3
- NumPy
- Biopython 1.85+
Execution
- info:Pinned dependenciesThe installation instruction uses `uv pip install biopython`, which typically installs the latest version but does not explicitly pin dependencies or provide a lockfile.
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-SkillsRuns the Vercel skills CLI (skills.sh) via npx — needs Node.js locally and at least one installed skills-compatible agent (Claude Code, Cursor, Codex, …). Assumes the repo follows the agentskills.io format.
Quality Score
VerifiedTrust Signals
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