biopython

Parse FASTA, GenBank, and PDB files using the Biopython library.

1|Updated Jan 14, 2026

Search Tags:#bioinformatics #genomics #sequence analysis #ncbi #biopython #phylogenetics

Ready to run

npx skills add https://github.com/Sologa/codex-pipeline --skill biopython-sologa

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: biopython
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/biopython
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill biopython-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill simplifies complex bioinformatics tasks, enabling efficient analysis of biological sequences, structures, and data from public databases.

Core Features & Use Cases

Sequence Manipulation: Work with DNA, RNA, and protein sequences.
File Parsing: Read and write common bioinformatics formats (FASTA, GenBank, PDB).
Database Access: Programmatically query NCBI databases (Entrez).
Structure Analysis: Parse and analyze 3D protein structures.
Phylogenetics: Build and visualize phylogenetic trees.
Use Case: Analyze a set of gene sequences, calculate their GC content, and find homologous sequences in the NCBI nr database.

Quick Start

Use the biopython skill to download the GenBank record for accession EU490707.

Frequently Asked Questions about biopython

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

FAQPage Schema

How do I parse and manipulate biological sequences from a FASTA file?▼

To parse and manipulate biological sequences from a FASTA file, this Skill reads standard bioinformatics formats and enables operations like translation or calculating GC content on the extracted DNA, RNA, or protein sequences.

Can I programmatically query NCBI Entrez databases to find homologous sequences?▼

Yes, you can programmatically query NCBI Entrez databases to find homologous sequences. This Skill facilitates automated database access to search and download records from public repositories like NCBI.

What is the best way to build and visualize phylogenetic trees from sequence data?▼

The best way to build and visualize phylogenetic trees from sequence data is using this Skill's integrated phylogenetics capabilities, which process aligned sequences to construct and render evolutionary trees.

Does this Skill support parsing 3D protein structures from PDB files?▼

Yes, this Skill supports parsing 3D protein structures from PDB files. It provides structural bioinformatics analysis tools to read, manipulate, and examine macromolecular structural data.

How do I read and write GenBank records for genomic analysis?▼

To read and write GenBank records for genomic analysis, this Skill parses the GenBank format to extract sequence features and annotations, enabling detailed computational molecular biology tasks.

What file formats are supported for computational molecular biology tasks?▼

Supported file formats for computational molecular biology tasks include FASTA, GenBank, and PDB. This allows seamless reading and writing of sequence, annotation, and structural data.