Does this skill support protein structure modeling?

It supports structural bioinformatics via the Bio.PDB module, allowing for the parsing of PDB files and calculation of structural properties.

What is the Biopython Claude Code Skill?

It is a specialized capability that enhances Claude's ability to write code and perform tasks related to biological computation using the Biopython library.

What are the requirements for using Biopython with Claude?

The environment requires Python 3 and the NumPy library to be installed for the Biopython tools to function correctly.

How does this skill handle BLAST searches?

It provides patterns for running BLAST searches via NCBI's web services and parsing the resulting XML output for downstream analysis.

Can Claude fetch sequences from GenBank using this skill?

Yes, the skill provides implementation patterns for using Bio.Entrez to programmatically search and download records from NCBI databases.

Biopython Bioinformatics

Name: Biopython Bioinformatics
Author: sanand0

bysanand0

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Data Science & ML

Streamlines computational molecular biology tasks including sequence analysis, NCBI database queries, and structural bioinformatics.

About

The Biopython skill equips Claude with the specialized knowledge required for industry-standard biological computation. It provides a robust framework for manipulating biological sequences (DNA, RNA, proteins), accessing NCBI databases like PubMed and GenBank programmatically via Bio.Entrez, and parsing complex file formats such as FASTA, PDB, and GenBank. Whether performing phylogenetic tree construction, protein structure analysis, or high-throughput BLAST searches, this skill ensures Claude applies best practices and optimized patterns for bioinformatics research and development.

Key Features

Comprehensive sequence manipulation, translation, and transcription
Phylogenetic tree construction and visualization workflows
Multi-format file parsing for FASTA, FASTQ, GenBank, and PDB
4 GitHub stars
Programmatic NCBI Entrez access for PubMed and GenBank queries
Protein structural analysis and RMSD calculation capabilities

Use Cases

Programmatically fetching and summarizing research publications for specific biological keywords
Automating the extraction and analysis of specific gene sequences from large GenBank datasets
Building automated pipelines for sequence alignment and phylogenetic tree generation

About

Key Features

Comprehensive sequence manipulation, translation, and transcription
Phylogenetic tree construction and visualization workflows
Multi-format file parsing for FASTA, FASTQ, GenBank, and PDB
4 GitHub stars
Programmatic NCBI Entrez access for PubMed and GenBank queries
Protein structural analysis and RMSD calculation capabilities

Use Cases

Programmatically fetching and summarizing research publications for specific biological keywords
Automating the extraction and analysis of specific gene sequences from large GenBank datasets
Building automated pipelines for sequence alignment and phylogenetic tree generation