How does this skill handle NCBI API rate limits?

The skill provides standardized patterns for setting your Entrez email and API keys, ensuring compliance with NCBI's rate-limiting policies and preventing IP blocks.

Which biological file formats are supported?

It supports a wide range of industry-standard formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, NEXUS, and Clustal.

Does it support BLAST searches?

Absolutely, it supports running remote NCBI BLAST queries via NCBIWWW and parsing the resulting XML output using NCBIXML for hit filtering.

Can I use this for protein structure analysis?

Yes, it includes specialized documentation for the Bio.PDB module to parse structure files, navigate the SMCRA hierarchy, and calculate molecular distances.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: plurigrid

byplurigrid

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Data Science & ML

Automates biological computation tasks including sequence analysis, structural bioinformatics, and programmatic NCBI database access.

The Biopython skill integrates the industry-standard Python library for computational biology into the Claude environment, enabling seamless processing of DNA, RNA, and protein data. It provides specialized guidance for parsing complex file formats like FASTA and GenBank, performing sequence alignments, interacting with the Entrez database for PubMed/NCBI queries, and analyzing 3D protein structures. This skill is essential for bioinformaticians and researchers looking to streamline molecular biology workflows using AI-assisted coding, sequence manipulation, and phylogenetic analysis.

Key Features

01Advanced BLAST workflow integration for running and parsing sequence searches

028 GitHub stars

03Programmatic NCBI database access via Bio.Entrez for automated record retrieval

04Sequence manipulation and translation for FASTA, GenBank, and FASTQ formats

05Phylogenetic tree construction, manipulation, and visualization capabilities

06Structural bioinformatics tools for analyzing PDB and mmCIF protein structures

Use Cases

01Building and visualizing phylogenetic trees from multiple sequence alignments

02Analyzing protein structure hierarchies to calculate atomic distances and identify motifs

03Automating the retrieval and parsing of gene sequences from NCBI for comparative genomics

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add plurigrid/asi biopython

For use in Claude.ai and ChatGPT

Download Skill