ucsc-genome-browser
Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. Retrieve sequence by region, list/fetch BED/bigWig tracks, chromosome sizes, RefSeq/GENCODE gene structures, PhyloP/PhastCons scores. Use for UCSC annotations; Ensembl REST API for Ensembl gene IDs and VEP variant annotation.
npx skills add BioTender-max/awesome-bio-agent-skills --skill ucsc-genome-browser --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.
# UCSC Genome Browser ## Overview The UCSC Genome Browser REST API at `https://api.genome.ucsc.edu/` provides programmatic access to genome sequences, annotation tracks, and hub data for 100+ assemblies including hg38, mm39, and dm6. The API is free, requires no authentication, and returns JSON. Use it with the `requests` library to fetch DNA sequences for genomic regions, retrieve track data (genes, repeats, conservation), list available tracks, and query chromosome sizes for genome-scale coordinate arithmetic. ## When to Use - Fetching the reference DNA sequence for any genomic region (e.g., promoter, exon, CRISPR target) across human, mouse, or other assemblies - Retrieving RefSeq or GENCODE gene structure (exon coordinates, CDS boundaries, strand) for a locus of interest - Looking up PhyloP or PhastCons conservation scores to assess evolutionary constraint at a variant site - Listing and querying any of UCSC's 1000+ annotation tracks (repeats, regulatory elements, conservation) for a region - Getting chromosome sizes for a genome assembly to set up bedtools, pysam, or coverage pipelines - Accessing public UCSC track hubs (e.g., ENCODE, Roadmap Epigenomics) without downloading d
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: Sequence Retrieval
- Query 2: Track Data Query
- Query 3: Track List
- Query 4: Chromosome Sizes
- Query 5: Gene Annotation
- Query 6: Conservation Scores
- Query 7: Hub Access
- Key Concepts
- 0-Based vs. 1-Based Coordinates
pip install requests matplotlib
What does the ucsc-genome-browser skill do?
Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. Retrieve sequence by region, list/fetch BED/bigWig tracks, chromosome sizes, RefSeq/GENCODE gene structures, PhyloP/PhastCons scores. Use for UCSC annotations; Ensembl REST API for Ensembl gene IDs and VEP variant annotation.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill ucsc-genome-browser --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.