How are NCBI rate limits managed?

The skill provides patterns for setting Entrez.email and using API keys to respect NCBI's usage policies while maximizing data retrieval speeds.

Can I use this skill to automate PubMed searches?

Yes, it utilizes the Bio.Entrez module to programmatically search, fetch, and parse publication data from PubMed and other NCBI databases.

Does it support 3D protein structure analysis?

Absolutely. It includes comprehensive tools for parsing PDB files, navigating the SMCRA structure hierarchy, and calculating distances or angles between atoms.

What biological file formats can this skill handle?

This skill supports a vast range of formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and NEXUS for sequence, structural, and phylogenetic data processing.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: pathvanasoftware

bypathvanasoftware

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Data Science & ML

Streamlines computational molecular biology tasks including sequence analysis, biological file parsing, and genomic database integration.

The Biopython skill empowers Claude to perform sophisticated bioinformatics operations by leveraging the comprehensive Biopython library. It provides specialized patterns for manipulating DNA, RNA, and protein sequences, parsing diverse biological file formats such as FASTA and GenBank, and programmatically interacting with NCBI databases through Entrez. This skill is ideal for researchers and developers building automated bioinformatics pipelines, performing structural protein analysis, or managing large-scale genomic datasets with precision and Pythonic efficiency.

Key Features

010 GitHub stars

02Phylogenetic tree construction and structural bioinformatics tools

03High-performance parsing for FASTA, GenBank, FASTQ, and PDB files

04Sequence manipulation, translation, and reverse complementation

05Automated BLAST search execution and XML result parsing

06Programmatic NCBI database access for PubMed and GenBank retrieval

Use Cases

01Automating batch sequence processing and GC content analysis for large datasets

02Fetching and converting genomic records from NCBI for local database construction

03Analyzing 3D protein structures to calculate residue distances and superimpose models

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add pathvanasoftware/iosstoragecleaner scientific-biopython

For use in Claude.ai and ChatGPT

Download Skill