biopython

Parse FASTA, GenBank, and PDB files with the Biopython toolkit.

Updated Mar 10, 2026

Search Tags:#bioinformatics #genomics #sequence analysis #biopython #phylogenetics #structural biology

Ready to run

npx skills add https://github.com/felixboehm/biochem-allergy --skill biopython-felixboehm

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: biopython
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/biopython
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill biopython-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill empowers users to perform complex computational molecular biology tasks programmatically, streamlining bioinformatics workflows and data analysis.

Core Features & Use Cases

Sequence Manipulation: Work with DNA, RNA, and protein sequences.
File Parsing: Read and write common bioinformatics file formats (FASTA, GenBank, PDB, etc.).
Database Access: Programmatically query NCBI databases (PubMed, GenBank, etc.).
Structure Analysis: Analyze protein structures and perform alignments.
Phylogenetics: Build and manipulate phylogenetic trees.
Use Case: Analyze a set of gene sequences, identify conserved regions, and build a phylogenetic tree to understand evolutionary relationships.

Quick Start

Use the biopython skill to fetch the GenBank record for accession number EU490707.

Frequently Asked Questions about biopython

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I parse FASTA and GenBank files for sequence analysis in Python?▼

To parse FASTA and GenBank files for sequence analysis in Python, use this Skill's built-in file handling capabilities. It reads and writes common bioinformatics formats, enabling programmatic interaction with biological data resources.

Can I query NCBI Entrez databases programmatically using Python?▼

Yes, you can query NCBI Entrez databases programmatically using Python. This Skill provides database access functionality to search and retrieve records from PubMed, GenBank, and other NCBI resources.

What's the best way to build a phylogenetic tree from DNA sequences in Python?▼

The best way to build a phylogenetic tree from DNA sequences in Python is using this Skill's phylogenetics module. It enables sequence manipulation to identify conserved regions and construct trees to understand evolutionary relationships.

Does this Python toolkit support protein structure analysis and PDB file parsing?▼

Yes, this Python toolkit supports protein structure analysis and PDB file parsing. It includes structural bioinformatics features to analyze protein structures, read PDB formats, and perform structural alignments.

How do I manipulate DNA, RNA, and protein sequences for custom bioinformatics pipelines?▼

To manipulate DNA, RNA, and protein sequences for custom bioinformatics pipelines, apply this Skill's sequence manipulation functions. It facilitates comprehensive computational molecular biology tasks, streamlining complex workflow analysis.

Do I need external dependencies to run computational molecular biology scripts with this toolkit?▼

No external dependencies are required to run computational molecular biology scripts with this toolkit. It operates independently with empty dependencies, providing a self-contained Python environment for custom bioinformatics pipelines.