The UCSC Genome Browser database: 2018 update

By Jonathan Casper, Ann S. Zweig, C. Villarreal, Cath Tyner, Matthew L. Speir, Kate R. Rosenbloom, Brian J. Raney, Christopher M. Lee, Brian T. Lee, Donna Karolchik and 14 more. 2017

454 citations recorded by the source corpus.

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

CADD: predicting the deleteriousness of variants throughout the human genome (2018, positive): “Annotations are obtained using Ensembl Variant Effect Predictor (VEP (15)), conservation and selection scores (e.g. PhyloP (16), PhastCons (17), GERP++ (18)), different tracks from the UCSC genome browser (19) as well as flat files of epigenetic information from the ENCODE and NIH RoadMap projects.”
Ensembl 2019 (2018, methodology): “We added support for two additional file formats: bigPsl for alignments (37) (https://genome.”
TransmiR v2.0: an updated transcription factor-microRNA regulation database (2018, methodology): “For intragenic miRNAs, we retrieved miRNA host genes from UCSC RefGene dataset (29), and 5′-end of the host gene was considered as the putative TSS.”
ClinVar: improvements to accessing data (2019, background): “In addition, links to genome browsers (NCBI’s Variation Viewer (7) and the UCSC browser (8)) have been added to this section, next to the genomic location, to make it easier to view the variant in its genomic context.”
CORUM: the comprehensive resource of mammalian protein complexes—2019 (2018, methodology): “At last, CORUM is cross-referenced by the UCSC-Genome browser (21) and UniProt (12).”
GENCODE reference annotation for the human and mouse genomes (2018, methodology): “GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.”
Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion (2018, background): “In addition, splicing patterns can be better understood by navigating existing transcript isoforms for a given gene in databases likeRefSeq, CCDS, Ensembl, and AceView (Casper et al., 2018;Harrison et al., 2017;O'Leary et al., 2016; Thierry-Mieg & Thierry-Mieg, 2006).”
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes (2019, methodology): “Bacterial, archaeal and 72 fungal eukaryotic genomes were obtained from NCBI GenBank, and 101 large eukaryotic genomes were obtained from the UCSC Genome Browser (21) and JGI Phytozome (22).”
CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens (2018, background): “As described in this year’s NAR database issue (5), the UCSC Genome Browser now contains a track ‘CRISPR’ that shows pre-computed CRISPOR results for various model organisms and the spCas9 nuclease.”
Genenames.org: the HGNC and VGNC resources in 2019 (2018, background): “HGNC symbols are displayed in all major databases containing human gene and protein data including Ensembl (1), NCBI Gene (2), UniProt (3), GeneCards (4) and the UCSC genome browser (5), as well as resources focused on human disease and phenotypes such as Decipher (6), OMIM (7), Locus Reference Geno”