What biological file formats does this skill support?

It supports a wide range of formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and more for both reading and writing operations.

How are NCBI rate limits handled?

The skill follows best practices by requiring an email address and supporting API keys to increase request limits from 3 to 10 requests per second.

Can I use this for real-time NCBI database searches?

Yes, it uses the Entrez module to programmatically search and fetch data from PubMed, GenBank, and other NCBI databases directly within your workflow.

Can I perform phylogenetic analysis with this skill?

Absolutely. It includes the Bio.Phylo and TreeConstruction modules for reading, writing, building, and visualizing phylogenetic trees.

Does it support structural biology analysis?

Yes, the Bio.PDB module allows for parsing, navigating, and performing calculations like distance and RMSD on 3D protein structures.

Biopython Scientific Toolkit

Name: Biopython Scientific Toolkit
Author: Blurjp

byBlurjp

데이터 과학 및 ML

Facilitates comprehensive computational molecular biology tasks including sequence manipulation, phylogenetic analysis, and programmatic database access.

소개

The Biopython skill integrates the powerful Biopython library into the Claude Code environment, enabling developers and researchers to perform complex bioinformatics tasks with ease. It provides standardized patterns for parsing biological file formats like FASTA and GenBank, conducting sequence alignments, interacting with NCBI databases through Entrez, and analyzing 3D protein structures via PDB modules. This skill is essential for automating bioinformatics pipelines, batch processing biological data, and performing structural or evolutionary analysis directly within a coding workflow.

주요 기능

Sequence manipulation and format conversion (FASTA, GenBank, FASTQ, PDB)
0 GitHub stars
Programmatic NCBI database access via Entrez for PubMed and GenBank
Phylogenetic tree construction, manipulation, and visualization
BLAST search automation and XML result parsing
Structural bioinformatics tools for PDB and mmCIF file analysis

사용 사례

Automating the retrieval and processing of genetic sequences from NCBI
Building custom bioinformatics pipelines for batch sequence alignment and analysis
Analyzing protein structures and calculating molecular properties from PDB files

소개

주요 기능

Sequence manipulation and format conversion (FASTA, GenBank, FASTQ, PDB)
0 GitHub stars
Programmatic NCBI database access via Entrez for PubMed and GenBank
Phylogenetic tree construction, manipulation, and visualization
BLAST search automation and XML result parsing
Structural bioinformatics tools for PDB and mmCIF file analysis

사용 사례

Automating the retrieval and processing of genetic sequences from NCBI
Building custom bioinformatics pipelines for batch sequence alignment and analysis
Analyzing protein structures and calculating molecular properties from PDB files