The UCSC Genome Browser database: extensions and updates 2013

By L. Meyer, Ann S. Zweig, A. Hinrichs, Donna Karolchik, Robert M. Kuhn, M. Wong, C. A. Sloan, Kate R. Rosenbloom, Greg Roe, B. Rhead and 22 more. Nucleic Acids Res., 2012

1,030 citations recorded by the source corpus.

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation ‘tracks’ are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

Subfields: Molecular Biology

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Citations in the corpus

Design and Analysis of Single-Cell Sequencing Experiments. (2015, background): “The genomic DNA sequence for most model organisms can be readily obtained from various online databases, such as the UCSC genome browser (Meyer et al., 2013) or www.ensembl. org (Cunningham et al., 2015).”
Gateways to the FANTOM5 promoter level mammalian expression atlas (2015, methodology): “Similarly, we prepared a set of configured data files for the data hub in the UCSC Genome Browser [40], which allow users to overlay the FANTOM5 CAGE peaks and TSS profiles with the views and annotations maintained by the database management team and the community.”
The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies (2017, neutral): “A limited HGMD data set, containing both chromosomal coordinates and HGMD identiﬁers, has been made available via academic data exchange programmes to the European Bioinformatics Institute (EBI)/Ensembl (Flicek et al. 2013) and the University of California, Santa Cruz (UCSC) (Meyer et al. 2013) and ”
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era (2012, methodology): “Rather than re-inventing the wheel, we decided to rely on the UCSC genome browser (19) as primary visualization platform.”
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014, background): “…spectrum disorders, epilepsy, Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, and stroke (Matute et al., 2005; Tian et al., 2005; Nagai et al., 2007; Chen et al., 2009; Li et al., 2011; Lioy et al., 2011; Molofsky et al., 2012; Zamanian et al., 2012).”
The UCSC Genome Browser database: 2014 update (2013, background): “The University of California Santa Cruz (UCSC) Genome Browser (1,2) at http://genome.”