The UCSC genome browser database: 2014 update

D Karolchik, GP Barber, J Casper… - Nucleic acids …, 2014 - academic.oup.com
D Karolchik, GP Barber, J Casper, H Clawson, MS Cline, M Diekhans, TR Dreszer, PA Fujita…
Nucleic acids research, 2014academic.oup.com
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 large collection of organisms, primarily vertebrates, with an emphasis on
the human and mouse genomes. The Browser's web-based tools provide an integrated
environment for visualizing, comparing, analysing and sharing both publicly available and
user-generated genomic data sets. As of September 2013, the database contained genomic …
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 large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser’s web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation ‘tracks’ for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.
Oxford University Press