Can I use this skill to download data from GenBank?

Yes, the skill includes implementation patterns for using Bio.Entrez to programmatically search and download sequences, features, and metadata from GenBank and other NCBI databases.

Does this skill help with protein structure analysis?

Yes, it provides tools for structural bioinformatics via the Bio.PDB module, allowing for the parsing of PDB/mmCIF files and calculation of distances, angles, and RMSD.

Does it support phylogenetic tree visualization?

Yes, the skill covers the Bio.Phylo module, which supports reading, manipulating, and visualizing phylogenetic trees in formats like Newick, NEXUS, and phyloXML.

What is the Biopython Claude Code Skill?

It is a specialized capability that provides Claude with the domain-specific logic and implementation patterns required to perform complex molecular biology tasks using the Biopython library.

Biopython Molecular Biology Toolkit

Name: Biopython Molecular Biology Toolkit
Author: Sologa

bySologa

0•

数据科学与机器学习

Streamlines computational molecular biology tasks including sequence analysis, biological file parsing, and programmatic NCBI database access.

The Biopython skill integrates the robust Biopython library into Claude's workflow, enabling sophisticated biological data processing and bioinformatics automation. It provides specialized patterns for sequence manipulation (DNA/RNA/Protein), phylogenetic tree construction, and structural bioinformatics using PDB files. This skill is particularly useful for researchers and developers building custom genomic pipelines, automating BLAST searches, or fetching batch records from NCBI databases via Entrez while adhering to programmatic best practices and rate limits.

主要功能

01BLAST search automation and XML result parsing

02Programmatic NCBI database access using Bio.Entrez with rate-limit management

03Comprehensive file parsing for FASTA, GenBank, FASTQ, and PDB formats

040 GitHub stars

05Automated sequence manipulation and translation (DNA/RNA/Protein)

06Structural bioinformatics and phylogenetic tree visualization tools

使用场景

01Batch downloading and processing publication data from PubMed and GenBank

02Analyzing protein structures and calculating molecular distances from PDB files

03Building automated bioinformatics pipelines for high-throughput sequence analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline biopython

For use in Claude.ai and ChatGPT

Download Skill