The UCSC Genome Browser Database: update 2006

By A. Hinrichs, Donna Karolchik, Robert Baertsch, Galt P. Barber, Gill Bejerano, Hiram Clawson, Mark Diekhans, Terrence S. Furey, Rachel A. Harte, Fan Hsu and 17 more. Nucleic Acids Res., 2005

2,062 citations recorded by the source corpus.

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at .

Subfields: Molecular Biology

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Citations in the corpus

The UCSC Genome Browser database: update 2011 (2010, background): “UCSC Genes, a gene prediction track generated at UCSC that is based on data from RefSeq, GenBank, CCDS and UniProt (2,7,8), is present for the most recent human and mouse assemblies.”
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs (2016, methodology): “de) at the MaxDelbr€ uck-Centrum f€ ur Molekulare Medizin (MDC), Berlin, Germany.(49)A complete list of all human circRNAs used in this study is available in the CircInteractome website.”
miRGen: a database for the study of animal microRNA genomic organization and function (2006, methodology): “All genome annotation files are downloaded from the UCSC genome annotation database (36) and all genome browser views are through the UCSC Genome Browser.”
Ensembl variation resources (2010, neutral): “As the genome browser at UCSC also uses the dbSNP variant mappings, using the same assembly is good for consistency across the major genome browsers.”
Circbank: a comprehensive database for circRNA with standard nomenclature (2019, methodology): “To perform the conservation analysis of human circRNA, we converted the coordinates of the backsplice site of each human circRNA to the mouse genome coordinates using the UCSC liftOver tool [33].”
The UCSC Genome Browser (2003, neutral): “…of other useful tools: BLAT ( Kent et al., 2002 ), for quickly mapping sequences to a genome assembly; the Table Browser ( Karolchik et al., 2004 ; Fujita et al., 2011 ), for viewing and manipulating the data underlying the Genome Browser; the Gene Sorter ( Kent et al., 2005 ), for exploring…”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, neutral): “Access through external databases ModBase models in academic and public datasets are also directly accessible from several databases, including the PMP (107), UniProtKB (109), PIR’s iProClass (103), EBI’s InterPro (105), the UCSC Genome Browser (104), PubMed (LinkOut) (110), PharmGKB (106) and SFLD ”
Genetic adaptation to high altitude in the Ethiopian highlands (2012, methodology): “We used genome-wide sequence data from several nonhuman primates (chimpanzee, orangutan, and rhesus macaque) downloaded from the UCSC Genome Browser website [42] to establish the ancestral allele for each of the SNPs included in our iHS analysis.”
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. (2007, methodology): “All alignments were masked for transposable elements using RepeatMasker annotations (Smit 1999) obtained from the UCSC Genome Browser Database (Hinrichs et al. 2006).”