The UCSC Genome Browser database: 2021 update

By Jairo Navarro Gonzalez, Ann S. Zweig, Matthew L. Speir, Daniel Schmelter, Kate R. Rosenbloom, Brian J. Raney, Conner C. Powell, Luis R. Nassar, Nathan D Maulding, Christopher M. Lee and 13 more. Nucleic Acids Res., 2020

438 citations recorded by the source corpus.

Abstract For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/186de699670b7b121077cf2129c9b8a508d4d159

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In Molecular Biology

1. Patricia P. Chan
2. Todd M. Lowe
3. Allysia J. Mak
4. Brian Y. Lin
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Citations in the corpus

• Variant interpretation using population databases: lessons from gnomAD (2021, background): “The asterix (*) marks the canonical transcript which is the Ensembl canonical transcript for v2 on GRCh37 and Matched Annotation from NCBI and EMBL ‐ EBI (MANE) Select transcript (Navarro Gonzalez et al., 2021) if available for v3 and later releases on GRCh38.”
• tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “Bacterial, archaeal and fungal genomes were obtained from NCBI GenBank (21) while the other eukaryotic genomes were obtained from the UCSC Genome Browser (22), NCBI GenBank (21), and JGI Phytozome (23).”