The UCSC Genome Browser database: extensions and updates 2011

By Timothy R. Dreszer, Donna Karolchik, Ann S. Zweig, A. Hinrichs, Brian J. Raney, Robert M. Kuhn, L. Meyer, M. Wong, C. A. Sloan, Kate R. Rosenbloom and 19 more. Nucleic Acids Res., 2011

406 citations recorded by the source corpus.

The University of California Santa Cruz 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, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. 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 new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced ‘track data hubs’, which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f995e0be49ba43b6d3324af2ee00c6a3be84d210

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Citations in the corpus

SIFT web server: predicting effects of amino acid substitutions on proteins (2012, methodology): “SIFT Indel was trained on a set of disease-causing frameshifting indels (3) and neutral indels derived from the UCSC pairwise alignments of the human genome with mammalian genomes (35).”
Early dissemination seeds metastasis in breast cancer (2016, positive): “Positions of the probes on the array were mapped to the current mouse reference genome (mm10) using the liftOver tool 47 .”
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014, positive): “…in the current genome; we detected 26 novel transcripts with expression levels of FPKM 5 that were previously unannotated in UCSC Genome Browser (Meyer et al., 2013), Ensembl (Flicek et al., 2012), Vega (Ashurst et al., 2005), and AceView (Thierry-Mieg and Thierry-Mieg, 2006) databases (data…”
Design and Analysis of Single-Cell Sequencing Experiments. (2015, positive): “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.”
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine (2013, positive): “A limited HGMD data set, containing both chromosomal coordinates and HGMD identiﬁers, has been made available via academic data exchange programmes to the Gen2Phen project (Webb et al. 2011), the European Bioinformatics Institute (EBI)/Ensembl (Flicek et al. 2013) and the University of California, S”
dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations (2013, methodology): “Among them, 89,572,881 contain hg18 coordinates, obtained via the liftOver tool from the UCSC Genome Browser (Meyer et al. 2012), to facilitate queries based on hg18.”
The UCSC genome browser and associated tools (2012, methodology): “Other features that use Javascript in the hgTracks CGI include drag-and-zoom and right-click track configuration, described previously [3].”
The Database of Genomic Variants: a curated collection of structural variation in the human genome (2013, methodology): “These data are accessed by multiple users and are the primary site for distributing the content to other genome databases including UCSC (13) and GeneCards (http://www.genecards.org/) and commercial vendors who use the data for both product development and as an annotation track in various software ”
A survey of tools for variant analysis of next-generation genome sequencing data (2013, neutral): “‘The Vertebrate Genome Annotation (Vega) Genome Browser’ [134] is built upon code of the Ensembl Genome Browser.”
Ensembl 2014 (2013, neutral): “As such, Ensembl provides unique tools, datasets and user support compared to similar projects such as the UCSC Genome Browser (1), while supporting community standards that promote interoperability in genomics.”