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Agent skill

Biopython Bioinformatics

by aiming-lab in aiming-lab/AutoResearchClaw

Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.

MITAuto-check passedResearch & Science

Install Biopython Bioinformatics

skills CLI
$ npx skills add aiming-lab/AutoResearchClaw --skill biology-biopython -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aiming-lab/AutoResearchClaw biology-biopython --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aiming-lab/AutoResearchClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/biology-biopython .claude/skills/biology-biopython && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
biology-biopython
GitHub stars
15k
Token cost
~810 tokens
SKILL.md length
322 words
Files
1
Skills in repo
34
Repo updated
First seen
Licence
MIT

At a glance

Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.

  • Works in 6 steps: Create sequences: from Bio.Seq import… → Complement: seq.complement(); Reverse… → Transcription: seq.transcribe() (DNA to… → …
  • Parsing, converting or indexing FASTA and GenBank files
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
  • Running a BLAST search and filtering the hits

What it does

The skill is organized as numbered how-to lists, each with the Biopython call to use. Sequence work covers complement, reverse complement, transcription, translation, GC content and molecular weight. SeqIO guidance covers reading, writing, converting and indexing FASTA and GenBank files. BLAST entries cover online searches through `NCBIWWW.qblast`, parsing results with `NCBIXML`, running local BLAST by subprocess, and filtering hits by e-value and coverage.

For NCBI access the agent is reminded to set `Entrez.email` first, to use an API key for higher rate limits, and to pause between batch requests. Further sections handle phylogenetic trees with `Bio.Phylo` in newick, nexus and phyloxml formats, and structure analysis with `Bio.PDB`, including mmCIF files. A pitfalls section warns that `SeqIO.parse` returns an iterator that is used up after one pass.

When your agent uses it

  • Parsing, converting or indexing FASTA and GenBank files
  • Running a BLAST search and filtering the hits
  • Fetching records from NCBI databases with Entrez
  • Reading and drawing phylogenetic trees or walking a PDB structure

Example prompts

  • “Convert genomes.gb to FASTA and report the GC fraction of each record.”
  • “Run a blastn search for this sequence against nt and keep hits with e-value below 1e-5.”
  • “Load tree.nwk and print the distance between the two deepest clades.”

Requirements

  • Python with Biopython
  • Network access to NCBI for online BLAST and Entrez
  • An email address for Entrez

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

  1. Create sequences: from Bio.Seq import Seq; seq = Seq("ATGCGA")
  2. Complement: seq.complement(); Reverse complement: seq.reverse_complement()
  3. Transcription: seq.transcribe() (DNA to RNA)
  4. Translation: seq.translate() (DNA/RNA to protein)
  5. GC content: from Bio.SeqUtils import gc_fraction; gc_fraction(seq)
  6. Molecular weight: from Bio.SeqUtils import molecular_weight

What it can do on your machine

Read from SKILL.md and the folder at commit be4ba47. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Biopython Bioinformatics loads about 810 tokens when it runs. Until then it costs about 47 tokens; SKILL.md has 322 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~47
When it runs · the whole SKILL.md, loaded when a task matches
~810

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from aiming-lab/AutoResearchClaw at commit be4ba47, republished under its MIT licence (© aiming-lab). 322 words, ~810 tokens.

Download SKILL.mdSave it as .claude/skills/biology-biopython/SKILL.md (or your agent's skills folder).
name
biology-biopython
description
Bioinformatics with Biopython for sequence manipulation, file parsing, BLAST, and phylogenetics. Use when working with DNA/RNA/protein sequences or biological databases.
metadata.category
domain
metadata.trigger-keywords
sequence,FASTA,genome,protein,BLAST,phylogenetic,biopython,bioinformatics,gene,DNA,RNA
metadata.applicable-stages
9,10,12
metadata.priority
4
metadata.version
1.0
metadata.author
researchclaw
metadata.references
adapted from K-Dense-AI/claude-scientific-skills

Biopython Bioinformatics Best Practice

Sequence Manipulation
  1. Create sequences: from Bio.Seq import Seq; seq = Seq("ATGCGA")
  2. Complement: seq.complement(); Reverse complement: seq.reverse_complement()
  3. Transcription: seq.transcribe() (DNA to RNA)
  4. Translation: seq.translate() (DNA/RNA to protein)
  5. GC content: from Bio.SeqUtils import gc_fraction; gc_fraction(seq)
  6. Molecular weight: from Bio.SeqUtils import molecular_weight
File Parsing (SeqIO)
  1. Read FASTA: for rec in SeqIO.parse("file.fasta", "fasta"): ...
  2. Read GenBank: for rec in SeqIO.parse("file.gb", "genbank"): ...
  3. Read single record: rec = SeqIO.read("file.fasta", "fasta")
  4. Write sequences: SeqIO.write(records, "output.fasta", "fasta")
  5. Convert formats: SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")
  6. Index large files: idx = SeqIO.index("large.fasta", "fasta") for random access
BLAST Operations
  1. Online BLAST: from Bio.Blast import NCBIWWW; result = NCBIWWW.qblast("blastn", "nt", seq)
  2. Parse results: from Bio.Blast import NCBIXML; records = NCBIXML.parse(result)
  3. Local BLAST: run via subprocess, parse XML output with NCBIXML
  4. Always set Entrez.email before any NCBI access
  5. Filter results by e-value (typically < 1e-5) and coverage
NCBI Database Access (Entrez)
  1. Always set email: Entrez.email = "your@email.com"
  2. Search: handle = Entrez.esearch(db="pubmed", term="query")
  3. Fetch records: handle = Entrez.efetch(db="nucleotide", id="ID", rettype="fasta")
  4. Use API key for higher rate limits (10 req/s vs 3 req/s)
  5. Respect NCBI rate limits; add delays between batch requests
Phylogenetics (Bio.Phylo)
  1. Read trees: from Bio import Phylo; tree = Phylo.read("tree.nwk", "newick")
  2. Draw trees: Phylo.draw(tree) or Phylo.draw_ascii(tree)
  3. Supported formats: newick, nexus, phyloxml
  4. Traverse clades: for clade in tree.find_clades(): ...
  5. Calculate distances: tree.distance(clade1, clade2)
Structure Analysis (Bio.PDB)
  1. Parse PDB: parser = PDBParser(); structure = parser.get_structure("id", "file.pdb")
  2. Hierarchy: Structure > Model > Chain > Residue > Atom
  3. Get atoms: iterate through structure.get_atoms()
  4. Calculate distances: use atom coordinate vectors
  5. For mmCIF files: use MMCIFParser() instead of PDBParser()
Common Pitfalls
  1. Always handle SeqIO.parse as an iterator — it exhausts after one pass
  2. Check sequence alphabet compatibility before operations
  3. Large files: use SeqIO.index() not SeqIO.to_dict() to avoid memory issues
  4. Set proper timeout for remote BLAST queries (can take minutes)
  5. Validate parsed data — missing annotations are common in public databases

© aiming-lab, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in .claude/skills/biology-biopython of aiming-lab/AutoResearchClaw.

Open the folder on GitHubat commit be4ba47

Compare with similar skills

Biopython Bioinformatics next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Biopython Bioinformatics compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Biopython Bioinformatics this skillaiming-lab/AutoResearchClaw15k—~810Automated safety check: PassMIT
Bio Entrez LinkGPTomics/bioSkills1.2k2 repos~3.8kAutomated safety check: PassMIT
Bio Write SequencesGPTomics/bioSkills1.2k3 repos~2.1kAutomated safety check: PassMIT
Biopythondavila7/claude-code-templates32k12 repos~3.4kAutomated safety check: PassMIT
Ggetdavila7/claude-code-templates32k10 repos~6.3kAutomated safety check: PassMIT
BiopythonK-Dense-AI/scientific-agent-skills48k1 repos~4.3kAutomated safety check: NotesMIT

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Works with

Categories

Questions about Biopython Bioinformatics

What does Biopython Bioinformatics do?

Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis. The skill is organized as numbered how-to lists, each with the Biopython call to use. Sequence work covers complement, reverse complement, transcription, translation, GC content and molecular weight.

When should I use Biopython Bioinformatics?

Biopython Bioinformatics fits situations like: parsing, converting or indexing FASTA and GenBank files; running a BLAST search and filtering the hits; fetching records from NCBI databases with Entrez; reading and drawing phylogenetic trees or walking a PDB structure.

How do I install Biopython Bioinformatics in Claude Code?

Run `npx skills add aiming-lab/AutoResearchClaw --skill biology-biopython -a claude-code`. Or copy the skill folder (.claude/skills/biology-biopython in aiming-lab/AutoResearchClaw) into .claude/skills/biology-biopython in your project. Claude Code loads it when a task matches its description.

How do I install Biopython Bioinformatics in Codex?

Run `npx skills add aiming-lab/AutoResearchClaw --skill biology-biopython -a codex`. Or copy the skill folder (.claude/skills/biology-biopython in aiming-lab/AutoResearchClaw) into .agents/skills/biology-biopython in your project. Codex loads it when a task matches its description.

Can I use Biopython Bioinformatics in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aiming-lab/AutoResearchClaw --skill biology-biopython -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/biology-biopython, .gemini/skills/biology-biopython, .github/skills/biology-biopython and .opencode/skills/biology-biopython in your project.

What does Biopython Bioinformatics need to run?

SKILL.md names no scripts, command-line tools or credentials: Biopython Bioinformatics is instructions for the agent only. Our summary lists: Python with Biopython; Network access to NCBI for online BLAST and Entrez; An email address for Entrez.

Does Biopython Bioinformatics access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Biopython Bioinformatics safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Biopython Bioinformatics use?

Biopython Bioinformatics is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Biopython Bioinformatics use?

About 810 tokens (SKILL.md is roughly 3.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Biopython Bioinformatics?

Skills that share tags, products or a category with Biopython Bioinformatics: Bio Entrez Link (GPTomics/bioSkills, 1.2k stars), Bio Write Sequences (GPTomics/bioSkills, 1.2k stars), Biopython (davila7/claude-code-templates, 32k stars) and Gget (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Biopython Bioinformatics?

aiming-lab (a GitHub organization) maintains it in aiming-lab/AutoResearchClaw, which has 14,602 GitHub stars. The repository holds 34 skills in this directory. The repository was last updated on August 19, 2026.

Source: aiming-lab/AutoResearchClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.