biopython-molecular-biology
Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
npx skills add BioTender-max/awesome-bio-agent-skills --skill biopython-molecular-biology --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Biopython: Computational Molecular Biology Toolkit ## Overview Biopython is the standard open-source Python library for computational molecular biology, providing modular APIs for sequence handling, biological file parsing, NCBI database access, BLAST searches, protein structure analysis, and phylogenetics. It supports Python 3 and requires NumPy. ## When to Use - Parse and convert biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, PHYLIP) - Fetch sequences or publications from NCBI databases (GenBank, PubMed, Protein) programmatically - Run and parse BLAST searches (remote NCBI or local BLAST+) - Perform pairwise or multiple sequence alignments with custom scoring - Analyze 3D protein structures — distances, angles, DSSP, superimposition - Build and visualize phylogenetic trees from sequence alignments - Calculate sequence statistics (GC content, molecular weight, melting temperature) - Batch-process thousands of sequences with custom filtering logic - Use `pysam` instead for reading SAM/BAM/CRAM alignment files and working with mapped reads; use `scikit-bio` instead for advanced ecological diversity metrics ## Prerequisites - **Python packages**: `biopython`, `numpy`,
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Module 1: Sequence Objects (Bio.Seq)
- Module 2: Sequence I/O (Bio.SeqIO)
- Module 3: NCBI Database Access (Bio.Entrez)
- Module 4: BLAST Operations (Bio.Blast)
- Module 5: Pairwise Alignment (Bio.Align)
- Module 6: Protein Structure Analysis (Bio.PDB)
- Module 7: Phylogenetics (Bio.Phylo)
- Module 8: Sequence Utilities (Bio.SeqUtils)
- Common Workflows
pip install biopython numpy matplotlib
What does the biopython-molecular-biology skill do?
Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill biopython-molecular-biology --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.