Can Biopython help with protein structure analysis?

Yes, it includes the Bio.PDB sub-package which allows for parsing, navigating, and performing calculations on 3D protein structures from PDB and mmCIF files.

Is an API key required for NCBI database access?

While not strictly required, using an API key increases your rate limit from 3 to 10 requests per second. However, providing a valid email address is mandatory for all Entrez queries.

What databases can I access with this Biopython skill?

You can programmatically access several NCBI databases including PubMed, GenBank, Protein, and Gene using the Bio.Entrez module within this skill.

Does this skill support sequence file format conversion?

Absolutely. Biopython handles reading, writing, and converting between a wide variety of formats including FASTA, GenBank, FASTQ, Clustal, and Phylip.

Biopython Bioinformatics Toolkit

Name: Biopython Bioinformatics Toolkit
Author: Microck

byMicrock

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Ciencia de Datos y ML

Enables advanced biological computation and molecular biology workflows using the Biopython library.

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The Biopython skill integrates comprehensive tools for biological computation into Claude's coding workflow, providing domain-specific guidance for molecular biology. It offers specialized support for sequence manipulation, file parsing for common bioinformatics formats like FASTA and GenBank, programmatic access to NCBI databases via Entrez, and complex structural or phylogenetic analyses. Whether you are automating BLAST searches, analyzing 3D protein structures, or building phylogenetic trees, this skill provides the necessary patterns and best practices for high-quality Python-based bioinformatics research.

Características Principales

Phylogenetic tree construction, manipulation, and visualization capabilities.
Programmatic NCBI/PubMed database access through Bio.Entrez with rate limiting.
89 GitHub stars
Sequence manipulation including translation, transcription, and reverse complement.
Support for reading and converting biological file formats (FASTA, GenBank, FASTQ, PDB).
Structural bioinformatics tools for parsing and analyzing 3D protein structures.

Casos de Uso

Automating large-scale sequence downloads and metadata analysis from NCBI databases.
Building automated pipelines for pairwise or multiple sequence alignment analysis.
Extracting and analyzing structural data from PDB files for molecular research.

Acerca de

Características Principales

Phylogenetic tree construction, manipulation, and visualization capabilities.
Programmatic NCBI/PubMed database access through Bio.Entrez with rate limiting.
89 GitHub stars
Sequence manipulation including translation, transcription, and reverse complement.
Support for reading and converting biological file formats (FASTA, GenBank, FASTQ, PDB).
Structural bioinformatics tools for parsing and analyzing 3D protein structures.

Casos de Uso

Automating large-scale sequence downloads and metadata analysis from NCBI databases.
Building automated pipelines for pairwise or multiple sequence alignment analysis.
Extracting and analyzing structural data from PDB files for molecular research.