Does it support structural bioinformatics?

Absolutely, it includes comprehensive support for Bio.PDB to parse 3D structures and calculate molecular distances, angles, and secondary structure assignments.

What file formats are supported?

It supports a wide range of bioinformatics formats including FASTA, GenBank, FASTQ, PDB, mmCIF, Newick, and BLAST XML results.

Can this skill help with NCBI Entrez queries?

Yes, it provides specific patterns for Bio.Entrez to search PubMed, GenBank, and other databases while respecting NCBI rate limits and requirements like email identification.

Can I use this for sequence alignment?

Yes, it provides implementation patterns for both pairwise and multiple sequence alignments using Bio.Align and Bio.AlignIO, including the use of substitution matrices.

Biopython Bioinformatics Toolkit

Name: Biopython Bioinformatics Toolkit
Author: Microck

byMicrock

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Data Science & ML

Streamlines computational molecular biology tasks including sequence analysis, NCBI database integration, and structural protein modeling.

This skill empowers Claude to perform complex bioinformatics workflows using the Biopython library. It provides expert guidance for manipulating biological sequences, parsing specialized file formats like FASTA and GenBank, conducting automated NCBI BLAST searches via Bio.Entrez, and analyzing 3D protein structures. Whether building phylogenetic trees or performing sequence alignments, this skill ensures Claude follows best practices for rate-limiting, data integrity, and efficient memory management in biological data processing.

Key Features

01Phylogenetic tree construction, manipulation, and visualization

02Parsing and conversion for FASTA, GenBank, PDB, and BLAST results

03Structural bioinformatics tools for 3D protein analysis and distance calculation

04Comprehensive sequence manipulation, translation, and transcription

05Programmatic NCBI database access via Bio.Entrez with rate-limiting

0681 GitHub stars

Use Cases

01Fetching and parsing publication and protein records from NCBI databases

02Automating large-scale genomic sequence analysis pipelines

03Analyzing protein structure properties and distances from PDB files

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills biopython

For use in Claude.ai and ChatGPT

Download Skill