Can I perform BLAST searches using this skill?

Yes, the skill provides patterns for running remote BLAST searches via NCBIWWW and parsing the resulting XML files using Bio.Blast.NCBIXML.

Which sequence file formats can this skill handle?

This skill supports all major biological formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Phylip, and Clustal through the Bio.SeqIO and Bio.AlignIO modules.

How does this skill handle large genomic files?

The skill follows best practices by using iterators (SeqIO.parse) rather than loading entire files into memory, ensuring efficient processing of large datasets.

Do I need an API key for NCBI database access?

While not strictly required, using an NCBI API key with Bio.Entrez increases your rate limit from 3 to 10 requests per second. Always remember to set your email address as required by NCBI.

What is the Biopython Claude Code Skill?

It is a specialized capability that allows Claude to write, debug, and optimize bioinformatics code using the Biopython library, covering tasks from sequence manipulation to structural biology.

Biopython Molecular Biology

Name: Biopython Molecular Biology
Author: Microck

byMicrock

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Ciencia de Datos y ML

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

Acerca de

Biopython is the industry-standard toolkit for computational molecular biology in Python, offering a robust set of libraries for biological data analysis. This skill enables Claude to manage complex bioinformatics workflows, ranging from sequence manipulation and file format conversion to advanced structural analysis, phylogenetic modeling, and high-throughput NCBI database queries. It provides domain-specific guidance on using modular sub-packages like Bio.Seq, Bio.Entrez, and Bio.PDB, ensuring best practices such as rate-limiting for API calls and memory-efficient file parsing are strictly followed.

Características Principales

Programmatic NCBI database access via Bio.Entrez for PubMed and GenBank searches
81 GitHub stars
Automated BLAST search integration and XML result parsing workflows
Comprehensive sequence manipulation and file I/O for FASTA, GenBank, and FASTQ
Advanced structural bioinformatics for parsing and analyzing PDB and mmCIF files
Phylogenetic tree construction, manipulation, and visualization tools

Casos de Uso

Analyzing protein structures to calculate residue distances and secondary structure assignments
Automating the batch download and conversion of genomic sequences from NCBI databases
Performing multiple sequence alignments and building phylogenetic trees for evolutionary studies

Acerca de

Características Principales

Programmatic NCBI database access via Bio.Entrez for PubMed and GenBank searches
81 GitHub stars
Automated BLAST search integration and XML result parsing workflows
Comprehensive sequence manipulation and file I/O for FASTA, GenBank, and FASTQ
Advanced structural bioinformatics for parsing and analyzing PDB and mmCIF files
Phylogenetic tree construction, manipulation, and visualization tools

Casos de Uso

Analyzing protein structures to calculate residue distances and secondary structure assignments
Automating the batch download and conversion of genomic sequences from NCBI databases
Performing multiple sequence alignments and building phylogenetic trees for evolutionary studies