Can this skill help with NCBI database access?

Yes, it provides optimized patterns for using Bio.Entrez to search and fetch data from NCBI databases like PubMed, GenBank, and Nucleotide.

Which biological file formats does this skill support?

It supports a wide range of formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and NEXUS through the SeqIO, PDB, and Phylo modules.

What is the Biopython Claude Code skill used for?

It is used to enhance Claude's ability to write and execute Python code for bioinformatics tasks, such as sequence analysis, phylogenetic tree building, and structural biology.

Does it support BLAST searches?

Yes, the skill includes guidance for running BLAST via NCBI's web services or local installations and parsing the resulting XML output.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: K-Dense-AI

byK-Dense-AI

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2,188

Data Science & ML

Performs complex biological computation, sequence analysis, and bioinformatics workflows using the Biopython library.

About

The Biopython skill empowers Claude to act as a specialized bioinformatics assistant, leveraging the industry-standard Biopython toolkit. It provides specific implementation patterns for sequence manipulation, file I/O for formats like FASTA and GenBank, and structural biology analysis. This skill is particularly useful for researchers needing to automate NCBI database queries via Entrez, manage BLAST workflows, analyze protein structures from PDB files, or construct phylogenetic trees, ensuring best practices in computational molecular biology are followed.

Key Features

Comprehensive sequence manipulation and translation (DNA/RNA/Protein)
Multi-format biological file parsing including FASTA, GenBank, and FASTQ
Phylogenetic tree construction, manipulation, and visualization
Programmatic NCBI database access via Bio.Entrez with rate-limit handling
Structural bioinformatics tools for parsing and analyzing PDB/mmCIF files
2,188 GitHub stars

Use Cases

Calculating molecular statistics and protein properties for large datasets
Building high-throughput sequence analysis and alignment pipelines
Automating the retrieval and parsing of genomic data from GenBank

About

Key Features

Comprehensive sequence manipulation and translation (DNA/RNA/Protein)
Multi-format biological file parsing including FASTA, GenBank, and FASTQ
Phylogenetic tree construction, manipulation, and visualization
Programmatic NCBI database access via Bio.Entrez with rate-limit handling
Structural bioinformatics tools for parsing and analyzing PDB/mmCIF files
2,188 GitHub stars

Use Cases

Calculating molecular statistics and protein properties for large datasets
Building high-throughput sequence analysis and alignment pipelines
Automating the retrieval and parsing of genomic data from GenBank