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Biopython Molecular Biology Toolkit

A skill that guides Claude to write correct Biopython code for sequence work, file parsing, NCBI access, BLAST, structures, and phylogenetics.

Data & AnalyticsIntermediate★ 41,485⑂ 3,824AI score 9/10Last updated: Aug 31, 2026

What it does

  • Builds sequence manipulation code for DNA/RNA/protein (transcription, translation, reverse complement) plus stats like GC content, molecular weight and melting temperature.
  • Reads, writes and converts FASTA, GenBank, FASTQ, PDB, mmCIF, Newick and other bioinformatics formats.
  • Queries NCBI databases (PubMed, GenBank, Protein, Gene) via Bio.Entrez, enforcing email/API-key and rate-limit etiquette.
  • Automates web and local BLAST runs, XML parsing, and E-value filtering.
  • Handles structural work with Bio.PDB (SMCRA navigation, distances, RMSD, DSSP) and trees with Bio.Phylo.
  • Ships module-specific reference docs (references/sequence_io.md, blast.md, structure.md, etc.) that Claude consults before writing code.

Who it's for

  • Researchers and grad students building their own bioinformatics pipelines.
  • Life-science practitioners doing batch sequence processing or paper reproduction.
  • Data analysts who repeatedly harvest and clean NCBI data.

Examples

  1. "Compute GC content and length for 3,000 sequences in this FASTA and export CSV" → memory-efficient SeqIO.parse iterator script.
  2. "Fetch EU490707 from GenBank and translate it to protein" → Entrez.efetch + SeqIO.read + translate().
  3. "Build a neighbor-joining tree from this alignment and print it as ASCII" → DistanceCalculator + DistanceTreeConstructor.nj + Phylo.draw_ascii.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/biopython/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on AI Skill Mart.
Copy the skills/biopython folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/biopython/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills && mkdir -p ~/.claude/skills && cp -r /tmp/scientific-agent-skills/skills/biopython ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills folder: mkdir -p ~/.claude/skills
  3. Copy the skill in: cp -r scientific-agent-skills/skills/biopython ~/.claude/skills/
  4. Install the Python dependency: uv pip install "biopython==1.87" (or pip install "biopython==1.87")
  5. For NCBI access, export credentials: export NCBI_EMAIL="your.email@example.com" and optionally export NCBI_API_KEY="..."
  6. Install local BLAST or MUSCLE separately if you plan to use the local-tool examples.
  7. Restart Claude Code and try a prompt like "parse this FASTA file" to confirm the skill loads.
View source on GitHub ↗License: MIT