What biological file formats does the Biopython skill support?

The Biopython skill supports a wide range of formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, NEXUS, and Clustal.

Does this skill support protein structure analysis?

Yes, the Bio.PDB module allows for parsing structure files, navigating the SMCRA hierarchy, and performing calculations like distance and dihedral angles.

Can I use this skill to search PubMed programmatically?

Yes, it utilizes the Bio.Entrez module to perform programmatic searches, fetch publication metadata, and download records from PubMed and other NCBI databases.

Do I need an API key for NCBI database access?

While not strictly required, using an Entrez API key is highly recommended to increase your rate limits from 3 to 10 requests per second.

Is NumPy required to use Biopython features?

Yes, Biopython depends on NumPy for many of its core computational tasks, particularly in structural bioinformatics and alignment analysis.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: Microck

byMicrock

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Ciencia de Datos y ML

Performs advanced biological computation, sequence analysis, and programmatic access to NCBI databases using Python.

Acerca de

Biopython is the industry-standard toolkit for computational molecular biology, providing Claude with the specialized knowledge to perform complex bioinformatics tasks. It streamlines sequence manipulation, structural analysis, and phylogenetic tree construction while offering robust tools for querying public databases like PubMed and GenBank via the Entrez system. This skill is essential for researchers and developers working on genomic analysis, protein modeling, or automated biological data processing pipelines within their development environment.

Características Principales

Programmatic NCBI database access via Bio.Entrez for automated PubMed and GenBank queries.
81 GitHub stars
Structural bioinformatics tools for navigating protein hierarchies and calculating atomic distances.
Robust parsing and analysis of standard formats including FASTA, GenBank, FASTQ, and PDB.
Phylogenetic tree manipulation, visualization, and distance calculation workflows.
Comprehensive sequence manipulation and translation for DNA, RNA, and protein data.

Casos de Uso

Developing pipelines for protein structure analysis and RMSD calculation using PDB files.
Automating the retrieval and statistical analysis of genomic sequences from NCBI databases.
Building and visualizing phylogenetic trees from multiple sequence alignment data.

Acerca de

Características Principales

Programmatic NCBI database access via Bio.Entrez for automated PubMed and GenBank queries.
81 GitHub stars
Structural bioinformatics tools for navigating protein hierarchies and calculating atomic distances.
Robust parsing and analysis of standard formats including FASTA, GenBank, FASTQ, and PDB.
Phylogenetic tree manipulation, visualization, and distance calculation workflows.
Comprehensive sequence manipulation and translation for DNA, RNA, and protein data.

Casos de Uso

Developing pipelines for protein structure analysis and RMSD calculation using PDB files.
Automating the retrieval and statistical analysis of genomic sequences from NCBI databases.
Building and visualizing phylogenetic trees from multiple sequence alignment data.