Agent skill · research science · k-dense-ai
biopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Why this skill is useful
Provides domain-specific commands and workflows for bioinformatics tasks that the AI wouldn't reliably generate on its own.
What it needs
Requires biopython, numpy installed locally. Requires ncbi account access. About 8k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
Biopython: Computational Molecular Biology in Python Overview Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is Biopython 1.87 (released 30 March 2026). It supports Python 3.10-3.14 and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses CVE-2025-68463 in Bio.Entrez.Parser when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML. When to Use This Skill Use this skill when: Working with biological sequences (DNA, RNA, or protein) Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.) Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez Running BLAST searches or parsing BLAST results Performing sequence alignments (pairwise or multiple sequence alignments) Analyzing protein structures from PDB files Creating, manipulating, or visualizing phylogenetic trees Finding sequence motifs or analyzing motif patterns Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.) Performing structural bioinformatics tasks Working with population genetics data Any other computational molecular biology task Core Capabilities Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains: 1. Sequence Handling - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O 2. Alignment Analysis - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments 3. Database Access - Bio.Entrez for programmatic access to NCBI databases 4. BLAST Operations - Bio.Blast for running and parsing BLAST searches 5. Structural Bioinformatics - Bio.PDB for working with 3D protein structures 6. Phylogenetics - Bio.Phylo for phylogenetic tree manipulation and visualization 7. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/biopython