The UCSC Genome Browser database: update 2011

By Pauline A. Fujita, B. Rhead, Ann S. Zweig, A. Hinrichs, Donna Karolchik, Melissa S. Cline, M. Goldman, Galt P. Barber, Hiram Clawson, A. Coelho and 17 more. Nucleic Acids Res., 2010

1,944 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

PhyLAT: a phylogenetic local alignment tool (2012, background): “In a recent update of the phylogenetic tree of 46 species from the UCSC database, 35 species changed their tree placements (Rhead, 2010).”
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data (2010, methodology): “Several different gene annotation systems, including RefSeq genes, UCSC Genes and the Ensembl genes, can be utilized for 13), ANNOVAR will download the FASTA sequences from Ensembl as they were not available from the UCSC Genome Browser.”
SFmap: a web server for motif analysis and prediction of splicing factor binding sites (2010, methodology): “SFmap output includes a link to the results in two different formats, both in text and in a visualized display of the motifs as custom annotation tracks in the UCSC human genome (HG) browser (15).”
The UCSC Genome Browser database: extensions and updates 2011 (2011, background): “A large number of summary tracks use the browser’s multi-colored overlay of wiggles method, introduced last year (2).”
Genome-wide enhancer maps link risk variants to disease genes (2021, methodology): “For all traits, except where specified, we considered only the ‘non-coding credible sets’—that is, those that did not contain any variant in a coding sequence or within 10 bp of a splice site annotated in the RefGene database (downloaded from UCSC Genome Browser on 24 June 2017) 58 .”
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse (2015, methodology): “Since the UCSC only implements the TFBS conservation tracks in human genome, we map the TFBS conservation information to mouse genome by employing the LiftOver (27) tool of UCSC.”
Chipster: user-friendly analysis software for microarray and other high-throughput data (2011, methodology): “Promoter sequences for human, mouse, rat, drosophila and yeast are obtained from the UCSC genome browser [30].”
miRcode: a map of putative microRNA target sites in the long non-coding transcriptome (2012, background): “To assess evolutionary conservation, a 46-way Multiz vertebrate genomic multiple alignment (Blanchette et al., 2004; Fujita et al., 2011) is remapped onto transcripts, and site conservation levels are determined based on site presence in primates, non-primate mammals and non-mammal vertebrates.”