skills.rest
biomaps-infra
biomaps-infraOFFICIAL
Explore all skills by this author →
GitHub

lib-biopython

Manipulate biological sequences and parse FASTA, GenBank, PDB, and mmCIF files.

Updated Mar 13, 2026
Search Tags:#bioinformatics#genomics#sequence analysis#biopython#phylogenetics#structural biology
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-biopython
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: lib-biopython
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/lib-biopython
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-biopython

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides a comprehensive Python toolkit for complex bioinformatics tasks, eliminating the need to write low-level code for sequence manipulation, database access, and structural analysis.

Core Features & Use Cases

  • Sequence Handling: Manipulate DNA, RNA, and protein sequences; parse common file formats (FASTA, GenBank).
  • Database Access: Programmatically query NCBI databases (PubMed, GenBank, Protein) via Bio.Entrez.
  • Structural Bioinformatics: Analyze 3D protein structures from PDB/mmCIF files.
  • Use Case: Analyze a set of protein sequences by fetching them from GenBank, performing a BLAST search, and then analyzing the resulting PDB structures for conserved motifs.

Quick Start

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

Frequently Asked Questions about lib-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, you can use this toolkit to programmatically read, manipulate, and extract biological data from standard sequence file formats without writing low-level code.

Can I query NCBI Entrez databases like PubMed and GenBank programmatically?▼

Yes, you can query NCBI Entrez databases like PubMed and GenBank programmatically, enabling automated retrieval of biological records and literature directly within your Python bioinformatics pipelines.

What is the best way to analyze 3D protein structures from PDB files?▼

The best way to analyze 3D protein structures from PDB and mmCIF files is using structural bioinformatics features that allow programmatic interaction with structural data to identify motifs and analyze molecular architecture.

Does this toolkit support building automated phylogenetic analysis pipelines?▼

Yes, this toolkit supports building automated phylogenetic analysis pipelines by providing Python tools for computational molecular biology, enabling programmatic interaction with biological sequence data for complex workflows.

How do I fetch a specific GenBank record by accession number?▼

To fetch a specific GenBank record by accession number, use the database access capabilities to query NCBI Entrez, retrieving the exact biological sequence and associated metadata for downstream analysis.

Related Skills

Explore More Education & Research Skills→
sanand0sanand0
8

biopython

Parse FASTA, GenBank, and PDB files for molecular biology analysis.

Community
Advanced
jimmc414jimmc414
557

scikit-bio

Analyze biological data with Python for sequences, phylogenetics, and statistics.

Community
Advanced
tassiovaletassiovale
13

scikit-bio

Manipulate biological sequences, alignments, trees, and diversity metrics in Python.

Community
Advanced
galeepgaleep

gget

Query over 20 genomic databases for gene and sequence data.

Community
Advanced