Is an API key required for NCBI database access?

While not strictly required, the skill recommends using an API key with Bio.Entrez to increase your rate limit from 3 to 10 requests per second.

What version of Biopython does this skill support?

The skill is optimized for Biopython 1.85 (released January 2025) and requires Python 3 and NumPy.

Can I use this to fetch data from NCBI?

Yes, it includes specialized patterns for the Bio.Entrez module to search and download records from PubMed, GenBank, and other NCBI databases.

Does it support protein structure analysis?

Yes, the skill provides patterns for the Bio.PDB module to parse, navigate, and analyze 3D protein structures using the SMCRA hierarchy.

How do I handle large genomic files efficiently?

The skill emphasizes using iterators like SeqIO.parse to process large FASTA or FASTQ files one record at a time to avoid memory exhaustion.

Biopython Molecular Biology Tools

Name: Biopython Molecular Biology Tools
Author: Activer007

byActiver007

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Data Science & ML

Facilitates computational molecular biology tasks including sequence analysis, NCBI database queries, and structural bioinformatics.

This skill empowers Claude to perform complex bioinformatics workflows by leveraging Biopython 1.85. It provides standardized patterns for manipulating DNA, RNA, and protein sequences, parsing diverse file formats like FASTA and GenBank, and programmatically accessing NCBI databases through Entrez. Whether you are performing pairwise alignments, analyzing 3D protein structures from PDB files, or constructing phylogenetic trees, this skill ensures best practices in biological computation and data handling within the Python ecosystem.

Key Features

01Programmatic NCBI database access via Bio.Entrez with rate-limit handling

020 GitHub stars

03Advanced sequence manipulation and file format conversion (FASTA, GenBank, FASTQ)

04Automated BLAST search execution and XML result parsing

05Structural bioinformatics tools for PDB and mmCIF file analysis

06Phylogenetic tree construction, manipulation, and visualization

Use Cases

01Modeling protein structures and calculating molecular distances or secondary structure assignments

02Automating sequence analysis pipelines for large-scale genomic data

03Fetching and parsing research data directly from PubMed, GenBank, and Protein databases

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills biopython

For use in Claude.ai and ChatGPT

Download Skill