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Biopython Molecular Biology Toolkit

Lets the agent write and run Biopython code for sequences, file formats, NCBI queries, BLAST, structures and trees.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
9 files

What it does

Once installed, the agent knows how to use Biopython, a widely used Python library for biology. It can read and convert sequence files (FASTA, GenBank, PDB), run alignments, search NCBI databases such as PubMed and GenBank through Bio.Entrez, run BLAST searches, analyse protein structures, and build phylogenetic trees. It follows the skill's reference guides and examples, which are pinned to Biopython 1.88 with notes on setup and rate limits.

Great for

  • Bioinformatics students learning to script sequence analysis
  • Researchers who want an agent to write batch scripts for FASTA/GenBank files or NCBI downloads
  • Developers building molecular biology pipelines in Python

Skip it if

  • Clinical or diagnostic decisions: the examples are illustrative and not validated for medical use
  • Large BLAST or Entrez jobs without care: remote services have rate limits and the skill itself warns about them
  • Users who expect the agent to run external tools automatically: BLAST, MUSCLE, Clustal Omega and DSSP need separate installs

Try asking

  • “Convert this GenBank file to FASTA and list the length of each record”
  • “Search PubMed for recent papers on CRISPR off-target effects and export the titles”
  • “Build a neighbour-joining tree from these aligned sequences and plot it”
  • “Calculate GC content and melting temperature for a list of primers”
Step-by-step guide: how to use Biopython Molecular Biology ToolkitInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 9 original files, the MIT licence and an attribution note.

    biopython.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip biopython.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip biopython.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Set NCBI_EMAIL and keep Entrez calls modest; use NCBI_API_KEY only if you need higher limits and keep it out of shared code
  • Ask the agent to review scripts before running them, especially ones that write files or call external services
  • Pin the Biopython version as the skill recommends so results stay reproducible

What's inside

  • references/advanced.md
  • references/alignment.md
  • references/blast.md
  • references/databases.md
  • references/phylogenetics.md
  • references/review.md
  • references/sequence_io.md
  • references/structure.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.