Skill · em Dados, IA e pesquisa

biopython

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/biopython
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

8 arquivos · 92,8 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/biopython/.

d=".claude/skills/biopython"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/biopython"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/alignment.md" "$u/references/alignment.md" \
  -o "$d/references/blast.md" "$u/references/blast.md" \
  -o "$d/references/databases.md" "$u/references/databases.md" \
  -o "$d/references/phylogenetics.md" "$u/references/phylogenetics.md" \
  -o "$d/references/sequence_io.md" "$u/references/sequence_io.md" \
  -o "$d/references/structure.md" "$u/references/structure.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/biopython/.

d="$HOME/.claude/skills/biopython"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/biopython"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/alignment.md" "$u/references/alignment.md" \
  -o "$d/references/blast.md" "$u/references/blast.md" \
  -o "$d/references/databases.md" "$u/references/databases.md" \
  -o "$d/references/phylogenetics.md" "$u/references/phylogenetics.md" \
  -o "$d/references/sequence_io.md" "$u/references/sequence_io.md" \
  -o "$d/references/structure.md" "$u/references/structure.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/biopython/.

d=".agents/skills/biopython"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/biopython"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/alignment.md" "$u/references/alignment.md" \
  -o "$d/references/blast.md" "$u/references/blast.md" \
  -o "$d/references/databases.md" "$u/references/databases.md" \
  -o "$d/references/phylogenetics.md" "$u/references/phylogenetics.md" \
  -o "$d/references/sequence_io.md" "$u/references/sequence_io.md" \
  -o "$d/references/structure.md" "$u/references/structure.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/biopython/.

d="$HOME/.agents/skills/biopython"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/biopython"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/alignment.md" "$u/references/alignment.md" \
  -o "$d/references/blast.md" "$u/references/blast.md" \
  -o "$d/references/databases.md" "$u/references/databases.md" \
  -o "$d/references/phylogenetics.md" "$u/references/phylogenetics.md" \
  -o "$d/references/sequence_io.md" "$u/references/sequence_io.md" \
  -o "$d/references/structure.md" "$u/references/structure.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/biopython/.

d=".agents/skills/biopython"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/biopython"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/alignment.md" "$u/references/alignment.md" \
  -o "$d/references/blast.md" "$u/references/blast.md" \
  -o "$d/references/databases.md" "$u/references/databases.md" \
  -o "$d/references/phylogenetics.md" "$u/references/phylogenetics.md" \
  -o "$d/references/sequence_io.md" "$u/references/sequence_io.md" \
  -o "$d/references/structure.md" "$u/references/structure.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/biopython/.

d="$HOME/.gemini/antigravity-cli/skills/biopython"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/biopython"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/alignment.md" "$u/references/alignment.md" \
  -o "$d/references/blast.md" "$u/references/blast.md" \
  -o "$d/references/databases.md" "$u/references/databases.md" \
  -o "$d/references/phylogenetics.md" "$u/references/phylogenetics.md" \
  -o "$d/references/sequence_io.md" "$u/references/sequence_io.md" \
  -o "$d/references/structure.md" "$u/references/structure.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.biopython

Prévia do SKILL.md

---
name: biopython
description: "Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database."
---

# Biopython: Computational Molecular Biology in Python

## Overview

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is **Biopython 1.85** (released January 2025), …

## When to Use This Skill

Use this skill when:

- Working with biological sequences (DNA, RNA, or protein)
- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
- Running BLAST searches or parsing BLAST results
- Performing sequence alignments (pairwise or multiple sequence alignments)
- Analyzing protein structures from PDB files
- Creating, manipulating, or visualizing phylogenetic trees
- Finding sequence motifs or analyzing motif patterns
- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
- Performing structural bioinformatics tasks
- Working with population genetics data
- Any other computational molecular biology task

## Core Capabilities

Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:

1. **Sequence Handling** - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
2. **Alignment Analysis** - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
3. **Database Access** - Bio.Entrez for programmatic access to NCBI databases
4. **BLAST Operations** - Bio.Blast for running and parsing BLAST searches
5. **Structural Bioinformatics** - Bio.PDB for working with 3D protein structures
6. **Phylogenetics** - Bio.Phylo for phylogenetic tree manipulation and visualization
7. **Advanced Features** - Motifs, population genetics, sequence utilities, and more
…

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