2015
DOI: 10.1093/nar/gkv1275
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The UCSC Genome Browser database: 2016 update

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, in… Show more

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Cited by 381 publications
(358 citation statements)
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“…Utilities from the University of California Santa Cruz (UCSC) genome browser source code tree (Speir et al ., 2016) were used to generate NET alignments from the raw pairwise alignments.…”
Section: Methodsmentioning
confidence: 99%
“…Utilities from the University of California Santa Cruz (UCSC) genome browser source code tree (Speir et al ., 2016) were used to generate NET alignments from the raw pairwise alignments.…”
Section: Methodsmentioning
confidence: 99%
“…For each exonic circRNA, we used the transcript structure of the longest 484 linear mRNA transcript of its host gene. We downloaded the PhastCons scores for the rat 485 genome from the UCSC genome browser database (Casper et al 2018). The base-by-base 486…”
Section: Evolutionary Analysis Of Rat Circrnas 481mentioning
confidence: 99%
“…29 Data were visualized using EaSeq. 30 The nucleotide sequences of regions with significantly altered H3K18Ac in Cbp D/D xEmBcl2 compared with Cbp F/F xEmBcl2 B cells were downloaded using the University of California, Santa Cruz Genome Browser 31 and interrogated for overrepresented DNA motifs and transcription factor binding sites using CisFinder. 32 For further details, refer to supplemental Methods.…”
Section: Chip-seqmentioning
confidence: 99%