[Show abstract][Hide abstract] ABSTRACT: For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information
from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous
development since its inception with new data sets and software features added frequently. Some release highlights of this
year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets;
improvements to track and assembly hub support; and a new interactive tool, the “Data Integrator”, for intersecting data from
multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include
updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more
genomic regulatory data, and a new multiple genome alignment.
Preview · Article · Jan 2015 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: 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.
Full-text · Article · Nov 2012 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: 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.
Full-text · Article · Nov 2011 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser
also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets,
aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track
drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay
of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’
windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights
include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA
editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.
Full-text · Article · Oct 2010 · Nucleic Acids Research