What biological file formats can this skill parse?

It handles a wide range of formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, NEXUS, and Clustal.

Does this skill support local BLAST searches?

Yes, the skill provides patterns for both running BLAST searches via NCBI's web services and executing local BLAST searches using command-line tools.

Can it be used for structural protein analysis?

Yes, it includes specialized documentation for the Bio.PDB module to calculate distances, angles, and perform structure superimpositions/RMSD calculations.

How does it handle NCBI API rate limits?

It implements best practices for Bio.Entrez, including setting required email headers and using API keys to increase rate limits from 3 to 10 requests per second.

Are there dependencies required to use this skill?

The skill assumes the presence of Biopython and NumPy, which can be installed via standard Python package managers like pip or uv.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

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

About

The Biopython skill equips Claude with specialized knowledge of the industry-standard Python toolkit for bioinformatics. It provides optimized implementation patterns for complex biological workflows, including parsing standard file formats like FASTA and PDB, programmatically querying NCBI databases via Entrez, automating BLAST searches, and performing structural or phylogenetic analyses. This skill is essential for researchers and developers automating genomic data processing, protein structure manipulation, or publication-grade sequence analysis within the Claude environment.

Key Features

Structural bioinformatics tools for 3D protein analysis and tree visualization
Programmatic NCBI database access for PubMed, GenBank, and Protein records
High-performance parsing for FASTA, GenBank, FASTQ, and PDB formats
Advanced biological sequence manipulation and protein translation
Comprehensive BLAST workflow automation and XML result parsing
1 GitHub stars

Use Cases

Performing structural proteomics analysis and phylogenetic tree construction
Automating large-scale genomic sequence analysis pipelines
Integrating NCBI data retrieval and citation management into research workflows

About

Key Features

Structural bioinformatics tools for 3D protein analysis and tree visualization
Programmatic NCBI database access for PubMed, GenBank, and Protein records
High-performance parsing for FASTA, GenBank, FASTQ, and PDB formats
Advanced biological sequence manipulation and protein translation
Comprehensive BLAST workflow automation and XML result parsing
1 GitHub stars

Use Cases

Performing structural proteomics analysis and phylogenetic tree construction
Automating large-scale genomic sequence analysis pipelines
Integrating NCBI data retrieval and citation management into research workflows