biopython
Analyze Molecular Biology Data with Biopython
Bioinformatics work often requires accurate parsing, database access, and reproducible analysis steps. This skill guides Claude, Codex, and Claude Code through practical Biopython workflows for molecular biology data.
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Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "biopython" from https://skillstore.io/skills/k-dense-ai-biopython.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-biopython/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "biopython". Summarize a FASTA file with many records.
Expected outcome:
- The response identifies the relevant SeqIO parser and format name.
- It recommends streaming records one at a time for large files.
- It describes a concise summary table with sequence identifiers, lengths, and descriptions.
Using "biopython". Fetch GenBank records from NCBI for a list of accessions.
Expected outcome:
- The response explains that Entrez email is required before requests.
- It outlines search or fetch steps, handle closing, and format choices.
- It notes rate limits and recommends caching downloaded records.
Using "biopython". Analyze distances in a PDB protein structure.
Expected outcome:
- The response selects Bio.PDB as the relevant module.
- It explains the structure, model, chain, residue, and atom hierarchy.
- It describes how to compare atom coordinates and report interpretable distances.
Security Audit
SafeAll static findings were adjudicated as false positives after reviewing the referenced documentation context. The skill is a Markdown guidance package for Biopython workflows, and I found no prompt injection, credential exfiltration, hidden execution, or malicious network intent.
Risk Factors
🔑 Env variables (4)
📁 Filesystem access (6)
🌐 Network access (6)
⚙️ External commands (50)
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<iframe src="https://skillstore.io/embed/skills/k-dense-ai-biopython.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). biopython security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-biopython/audits/7BibTeX citation
@techreport{k-dense-ai-k-dense-ai-biopython-2026,
author = {K-Dense-AI},
title = {biopython security audit report (audit version 7)},
institution = {Skillstore},
year = {2026},
number = {7},
url = {https://skillstore.io/skills/k-dense-ai-biopython/audits/7},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "biopython security audit report (audit version 7)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-05"
url: "https://skillstore.io/skills/k-dense-ai-biopython/audits/7"
identifiers:
- type: other
value: "skillstore:k-dense-ai-biopython:audit:7"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
k-dense-ai-biopython
2026-08-21
davila7-biopython
2026-08-21
Skillstore Score
Why this score Evidence Confidence: HighWhat You Can Build
Process sequence datasets
Parse FASTA or GenBank files, calculate sequence properties, convert formats, and stream large datasets efficiently.
Retrieve NCBI records
Search PubMed or GenBank, fetch records, follow related database links, and respect NCBI usage requirements.
Inspect protein structures
Read PDB or mmCIF files, navigate chains and residues, calculate distances, and export selected structure regions.
Try These Prompts
Show me how to read a FASTA file with Biopython and summarize each sequence identifier, length, and description.
Help me search NCBI PubMed for a biology topic, fetch the first results, and explain the required Entrez settings.
Create a Biopython workflow that runs a BLAST search, saves the result, parses top hits, and filters them by E-value.
Design a reproducible Biopython pipeline that converts GenBank records to FASTA, aligns sequences, builds a tree, and records parameters.
Best Practices
- Set Entrez email and respect NCBI rate limits before using online database examples.
- Use iterators and streaming parsers for large biological files.
- Record file formats, thresholds, database names, and tool versions for reproducible analysis.
Avoid
- Do not hardcode real API keys or personal contact details in shared scripts.
- Do not run large repeated web BLAST or Entrez requests without caching results.
- Do not assume parser format names match files without checking the input format.
Frequently Asked Questions
What is this skill for?
Does it install Biopython automatically?
Can it access NCBI databases?
Does it support BLAST workflows?
Can it analyze protein structures?
Is it suitable for very large datasets?
Developer Details
Author
K-Dense-AILicense
Unknown
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/biopythonRef
a25199bc7d6b82598536822d1738eb5d5f54025b
Maintenance freshness
7/18/2026
Usage
5 downloads · 542 views
File structure