The UCSC genome browser and associated tools

By Robert M. Kuhn, David Haussler, W. James Kent. Briefings Bioinform., 2012

840 citations recorded by the source corpus.

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e7adf166b24fdd8574f86a69ccf2ed69a38450cb

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

RCircos: an R package for Circos 2D track plots (2013, methodology): “We use the chromosome ideogram tables from UCSC genome browser to generate chromosome ideogram images and currently human, mouse, and rat are available in RCircos, but other species can be supported if relevant ideogram table is provided in a same format as cytoBandIdeo table in the UCSC genome brow”
The UCSC Genome Browser database: 2015 update (2014, methodology): “A UCSC assembly ID is assigned using the first three characters of the genus and species, plus a number (for earlier assemblies, just the first character of genus and species) (53).”
M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity (2016, background): “Overlap between HGMD and ExAC consists mostly of recessive mutations that are tolerated in the heterozygous state and misannotations 10 .”
The Ensembl Regulatory Build (2015, methodology): “These three sets of regions were remapped from GRCh37 to GRCh38 using liftOver [50].”
Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. (2017, positive): “We annotated human breakpoint coordinates against RefSeq and UCSC gene annotations (downloaded from the UCSC genome browser on 30Jun-2013) (Kuhn et al., 2013).”
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era (2012, methodology): “The specific objectives of EPDnew are: (i) to provide comprehensive and high-quality promoter collections for a number of eukaryotic model organisms; and (ii) to provide integrated views of promoter-defining evidence and other promoter-relevant information by means of custom track files that can be ”
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. (2018, positive): “After lifting over human SNPs to orthologous coordinates in themouse genome (Kuhn et al., 2013), we calculated the enrichment of heritability for 32 phenotypes across the DA peaks obtained for each of our 85 clusters (Figure 7A andAdditional Resources).”
CrossMap: a versatile tool for coordinate conversion between genome assemblies (2014, background): “Received on October 28, 2013; revised on December 4, 2013; accepted on December 12, 2013”
Spatiotemporal analysis of human intestinal development at single-cell resolution (2021, positive): “Raw 10X scRNA-seq and spatial transcriptomics raw sequence data processing Human hg38 reference genome analysis set was downloaded from the University of California Santa Cruz (UCSC) ftp site (Kuhn et al., 2013).”
dbSUPER: a database of super-enhancers in mouse and human genome (2015, methodology): “The interface also provides a link to visualize data in UCSC genome browser (39) by adding custom tracks automatically.”
Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma (2017, positive): “Human genes involved in the integration are identified using the breakpoint coordinates based on RefSeq and UCSC gene annotations (last modified on 30-Jun-2013) from the UCSC genome browser.”