The UCSC Genome Browser Database: update 2009

By Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Ting Wang, Kayla E. Smith, Kate R. Rosenbloom, B. Rhead, Brian J. Raney, A. Pohl, Michael Pheasant and 12 more. Nucleic Acids Res., 2008

679 citations recorded by the source corpus.

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/54f4ef17f6b7a315260e001af85fc8b6fc1d2a7b

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In Molecular Biology

1. David P. Bartel
2. Heng Li
3. Steven L. Salzberg
4. David Haussler
5. Richard Durbin
6. W. James Kent
7. Robert M. Kuhn
8. Eugene Berezikov

Citations in the corpus

• AltAnalyze and DomainGraph: analyzing and visualizing exon expression data (2010, background): “AltAnalyze augments this set of Ensembl exons with exons and corresponding genomic coordinates from the UCSC genome database of mRNA transcripts (7) and domain/motif annotations from the UniProt database.”
• Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. (2010, positive): “…analysis, a candidate was considered broadly conserved if the hairpin structure and the seed sequence were conserved to chickens, fish, frogs, or lizards (galGal3, danRer5, xenTro2, and anoCar1, respectively) in the University of California at Santa Cruz whole-genome alignments (Kuhn et al. 2009).”
• Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. (2007, positive): “All alignments were masked for transposable elements using RepeatMasker annotations (Smit 1999) obtained from the UCSC Genome Browser Database (Hinrichs et al. 2006).”
• The UCSC Genome Browser Database: 2008 update (2007, background): “edu) (1) provides a common repository for genomic annotation data—including comparative genomics, genes and gene predictions; mRNA and EST alignments; and expression, regulation, variation and assembly data—and robust, flexible tools for viewing, comparing, distributing and analyzing the information”
• Ensembl variation resources (2010, neutral): “Ensembl [11], University of California at Santa Cruz (UCSC) [12,13] and the National Center for Biotechnology Information (NCBI) [14] have expertise in the storage and manipulation of biological data and have developed genome browsers and other methods to archive and display these data alongside…”
• Chipster: user-friendly analysis software for microarray and other high-throughput data (2011, positive): “Promoter sequences for human, mouse, rat, drosophila and yeast are obtained from the UCSC genome browser [30].”
• Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome (2008, methodology): “. Refseq18 annotations were used to determine reading frame; regions that mapped to multiple Refseq genes were excluded if two or more of these genes were out-of-frame (89 kb of the 18.3 Mb of aligned regions). Furthermore, isPCR”
• Fast Computation and Applications of Genome Mappability (2012, positive): “Visualization of mappability on the UCSC browser [7]: the example of the human TK1 gene.”
• UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs (2009, background): “The gene-centric structure of UTRdb facilitates a full integration with all possible gene attributes collected in the NCBI Gene database (8) or other genomic resources such as the UCSC genome browser (9).”
• Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. (2009, methodology): “These UCSC Genome Browser alignments were also used to generate EPAs at each position, because they cover 44 diverse vertebrate species, including agnathans, fishes, amphibians, birds, and mammals (http://genome.ucsc.edu/).”
• PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. (2007, methodology): “For the reasons described above, we caution that despite the higher resolution of SNP genotyping arrays in detecting CNVs, different (Kuhn et al. 2007) shots of the CNVs within the FBXL7 ( A ), EYA1 ( B ), and CTDSPL ( C ) genes, as well as the location of SNPs and PCR primers.”
• Identifying Mendelian disease genes with the Variant Effect Scoring Tool (2013, positive): “Indels were mapped onto RefSeq proteins using the refGene table in the UCSC Genome Browser [50].”