The main public genome databases for browsing, downloading and annotating genome sequences. Each entry below links to the official resource with a note on what it’s best for.
Core genome browsers and databases
- Ensembl — genome browser and annotation for vertebrates and model organisms, with comparative genomics, variation and a powerful BioMart export. (Non-vertebrates: Ensembl Genomes.)
- UCSC Genome Browser — fast, track-rich browser; excellent for visualising annotations, conservation and your own data via custom tracks and the Table Browser.
- NCBI Datasets / Genome — reference genomes, RefSeq curated sequences, and bulk download of assemblies and annotations.
- GENCODE — the reference gene annotation for human and mouse used by ENCODE and many pipelines.
Specialised resources
- IGSR / 1000 Genomes — human genetic variation across populations.
- JGI — plant, fungal, microbial and environmental genomes.
- NCBI Genome — organism-centric genome overviews and assemblies.
Which should I use?
For gene annotation and comparative genomics, start with Ensembl; for fast visualisation and custom tracks, UCSC; for reference assemblies and programmatic download, NCBI Datasets/RefSeq. They are complementary — most projects use more than one.
Frequently asked questions
What is the best genome browser?
Ensembl and the UCSC Genome Browser are the two most widely used; Ensembl is strong on annotation and comparative genomics, UCSC on visualisation and custom tracks.
Where do I download a reference genome?
From NCBI Datasets/RefSeq, Ensembl, or UCSC — each provides assemblies and annotation files (FASTA, GTF/GFF).
What is RefSeq?
NCBI’s curated, non-redundant set of reference sequences for genomes, transcripts and proteins.
