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Cited by 883Genomics and Phylogenetic StudiesGenetics, Bioinformatics, and Biomedical ResearchBioinformatics and Genomic Networks

The UCSC genome browser and associated tools

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Kuhn, R. M., Haussler, D., Kent, W. J.·2013·Briefings in Bioinformatics
DOI 10.1093/bib/bbs038PMC PMC3603215
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Abstract

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.

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  • Imputed genetic variants were filtered for INFO > 0.7 and chromosome positions were lifted to the hg38 build using LiftOver.

    “Imputed genetic variants were filtered for INFO > 0.7 and chromosome positions were lifted to the hg38 build using LiftOver 58 .”

    From Plasma proteomic associations with genetics and health in the UK Biobank (2023) · cites this paper as [58]

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Research works printed but not linked: 44

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Authors
Kuhn, R. M., Haussler, D., & Kent, W. J.
Affiliations
  • University of California, Santa Cruz (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
Kuhn, R. M.
ORCID
Venue
Briefings in Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2012-08-20
Volume
14
Issue
2
Pages
144-161
ISSN
  • 1467-5463 (ISSN-L)
  • 1477-4054
DOI
10.1093/bib/bbs038
PMC
PMC3603215
OpenAlex
W2132522861
Cited by
883
References
5
Citations by year
2026: 63 · 2025: 81 · 2024: 95 · 2023: 106 · 2022: 97 · 2021: 101 · 2020: 77 · 2019: 53 · 2018: 44 · 2017: 29 · 2016: 30 · 2015: 34 · 2014: 40 · 2013: 32 · 2012: 1
FWCI
12.88
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Briefings in Bioinformatics (publishedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Howard Hughes Medical Institute
  • National Human Genome Research Institute (P01HG005062, U01HG004695, P41HG002371, U41HG004269, U41HG004568)
  • National Institute of Environmental Health Sciences (U01ES017154)
  • National Institute of Child Health and Human Development
  • National Institute of Dental and Craniofacial Research (U01DE020057)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (RC2HD064525)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
UCSC Genome Browser, genome visualization, genome annotation, blat, variant visualization, conservation scores, whole-genome alignment, high-throughput sequencing data, RNA-seq, ChIP-seq, data mining
MeSH terms
Animals, Computer Graphics, Data Display, Humans, Software, Information Storage and Retrieval, Sequence Alignment, Computational Biology, Internet, Genomics, Databases, Genetic, Data Mining, Search Engine

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