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. 2018 Jan 4;46(D1):D762-D769.
doi: 10.1093/nar/gkx1020.

The UCSC Genome Browser database: 2018 update

Jonathan Casper  1 , Ann S Zweig  1 , Chris Villarreal  1 , Cath Tyner  1 , Matthew L Speir  1 , Kate R Rosenbloom  1 , Brian J Raney  1 , Christopher M Lee  1 , Brian T Lee  1 , Donna Karolchik  1 , Angie S Hinrichs  1 , Maximilian Haeussler  1 , Luvina Guruvadoo  1 , Jairo Navarro Gonzalez  1 , David Gibson  1 , Ian T Fiddes  1 , Christopher Eisenhart  1 , Mark Diekhans  1 , Hiram Clawson  1 , Galt P Barber  1 , Joel Armstrong  1 , David Haussler  1   2 , Robert M Kuhn  1 , W James Kent  1
Affiliations

The UCSC Genome Browser database: 2018 update

Jonathan Casper et al. Nucleic Acids Res. .

Abstract

The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

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Figures

Figure 1.
Figure 1.
CRISPR/Cas9 Track. This track displays binding sites for the CRISPR/Cas9 complex that fall in transcribed regions or within 200 bp of such regions. Sites are scored for predicted cleavage efficiency and specificity and colored accordingly. Green sites have high predicted cleavage efficiency and specificity. Gray sites have low specificity.
Figure 2.
Figure 2.
Gene Interactions Tool. This tool displays the network of gene interactions as determined from a collection of 23 pathway and protein-interaction databases, in tandem with text-mining of abstracts on PubMed. Hovering over the edge between two genes (shown) shows information about the interaction between them. Clicking on an edge provides more details on a separate page.
Figure 3.
Figure 3.
New Genotype-Tissues Expression (GTEx) track interface. The previous checklist interface remains on the left. The body map on the right is interactive; hovering the mouse pointer over a tissue name will highlight that tissue in the body map image. Tissue names can be clicked to activate or deactivate that tissue in the track display, just as with the checklist.
Figure 4.
Figure 4.
Example hub search results. This shows an example track hierarchy in the search results for the GTEx RNA-seq hub, looking for tracks that match the term ‘amygdala’. The highlighted track has been right-clicked, and clicking the ‘Configure this track’ link will connect to the hub and open the configuration page for that track.
Figure 5.
Figure 5.
Example of highlighting multiple features with different colors. This image shows the OPN1LW, OPN1MW and OPN1SW genes from chrX and chr7 brought together using the Browser's multi-region mode, each with its own highlight.
See this image and copyright information in PMC

References

    1. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler D.. The Human Genome Browser at UCSC. Genome Res. 2002; 12:996–1006. - PMC - PubMed
    1. Haeussler M., Schönig K., Eckert H., Eschstruth A., Mianné J., Renaud J.-B., Schneider-Maunoury S., Shkumatava A., Teboul L., Kent J. et al. . Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016; 17:148. - PMC - PubMed
    1. Bae S., Kweon J., Kim H.S., Kim J.-S.. Microhomology-based choice of Cas9 nuclease target sites. Nat. Methods. 2014; 11:705–706. - PubMed
    1. Moreno-Mateos M.A., Vejnar C.E., Beaudoin J.-D., Fernandez J.P., Mis E.K., Khokha M.K., Giraldez A.J.. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods. 2015; 12:982–988. - PMC - PubMed
    1. Doench J.G., Fusi N., Sullender M., Hegde M., Vaimberg E.W., Donovan K.F., Smith I., Tothova Z., Wilen C., Orchard R. et al. . Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 2016; 34:184–191. - PMC - PubMed

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