What biological file formats does this skill support?

It supports a wide range of formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and NEXUS for sequence, structural, and phylogenetic data.

Is an API key required for NCBI access?

An API key is optional but recommended; it increases the rate limit from 3 to 10 requests per second, which is beneficial for large-scale data retrieval.

Does this skill handle protein structure analysis?

Yes, it includes the Bio.PDB module for parsing structure files, navigating the SMCRA hierarchy, and calculating molecular distances or RMSD.

Can I use this skill to search PubMed programmatically?

Yes, the skill utilizes Bio.Entrez to perform searches and fetch records from NCBI databases, including PubMed, GenBank, and Gene.

Biopython Molecular Biology Toolkit

Name: Biopython Molecular Biology Toolkit
Author: Yezez9

byYezez9

0•

数据科学与机器学习

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

The Biopython skill for Claude Code provides a specialized suite of tools for computational molecular biology, enabling seamless integration of sequence manipulation, structural bioinformatics, and phylogenetic analysis into AI-assisted workflows. It streamlines complex tasks such as parsing diverse file formats like FASTA and GenBank, performing programmatic NCBI searches via Entrez, and automating BLAST operations, making it an essential resource for researchers and bioinformaticians building automated data pipelines.

主要功能

01Programmatic NCBI database access for PubMed and GenBank via Bio.Entrez

02Comprehensive sequence manipulation and I/O for FASTA, GenBank, and FASTQ formats

03Phylogenetic tree construction, manipulation, and visualization capabilities

04Automated BLAST search execution and sophisticated XML result parsing

050 GitHub stars

06Structural bioinformatics tools for PDB and mmCIF protein file analysis

使用场景

01Analyzing protein structures and calculating molecular distances for structural biology

02Programmatically fetching and summarizing research data from PubMed and NCBI

03Automating batch processing for genomic sequence analysis pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent biopython

For use in Claude.ai and ChatGPT