The UCSC Genome Browser database: 2024 update

Abstract

The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to SARS-CoV2. This year, we have introduced new data from the Human Pangenome Reference Consortium and on viral genomes including SARS-CoV2. We have added 1,200 new genomes to our GenArk genome system, increasing the overall diversity of our genomic representation. We have added support for nine new user-contributed track hubs to our public hub system. Additionally, we have released 29 new tracks on the human genome and 11 new tracks on the mouse genome. Collectively, these new features expand both the breadth and depth of the genomic knowledge that we share publicly with users worldwide.

Graphical Abstract

Figure 1.

Browser view of a section of hg38 chromosome 2 where the HPRC Inversions summary track shows that there are two inversions in the HPRC genomes. Also shown are four chain tracks for both chromosomes of two individuals (HG00741, HG01928) showing that each individual has one parent with the inversion, whereas the other parent doesn’t.

Figure 2.

Illustration of the squishyPack display mode on the GENCODE gene set.

Figure 3.

Sequence logos summarizing the genomic conservation at each genomic position. The height of each letter at each position describes the conservation at that position and the observed nucleotides.

Figure 4.

Illustration of Rearrangement Mode, displaying a region on hg38 chromosome 10 where a block is inverted in the pairwise alignment of a BLAT query sequence and in an alignment to Chimps chromosome 10.

Figure 5.

Decorator visualization of EF-Hand domains in the gene SELENON. The upper transcript annotation, in blue, was generated by TrEMBL, while the lower two transcripts in red are annotated by Swiss-Prot. A cyan diamond in the right exon marks the location of a selenocysteine.