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PMID: 24227676 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Bioinformatics (Oxford, England) ·Vol. 30 ·No. 7 ·2014-04-01 ·Pages 1003-5

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ

Abstract

Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu.

MeSH Terms

Databases, Genetic Genome Genomics/methods Internet Software

Authors & Affiliations

11 authors, click to expand affiliations / ORCID

Raney Brian J

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA and Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.

Dreszer Timothy R

Barber Galt P

Clawson Hiram

Fujita Pauline A

Wang Ting

Nguyen Ngan

Paten Benedict

Zweig Ann S

Karolchik Donna

Kent W James

References (9)

9 references, click to expand

BigWig and BigBed: enabling browsing of large distributed datasets.
Bioinformatics. 2010 Sep 1;26(17):2204-7 PMID: 20639541
The distributed annotation system.
BMC Bioinformatics. 2001;2:7 PMID: 11667947
The UCSC Table Browser data retrieval tool.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6 PMID: 14681465
Ensembl 2013.
Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55 PMID: 23203987
The variant call format and VCFtools.
Bioinformatics. 2011 Aug 1;27(15):2156-8 PMID: 21653522
The human genome browser at UCSC.
Genome Res. 2002 Jun;12(6):996-1006 PMID: 12045153
The UCSC Genome Browser database: extensions and updates 2013.
Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9 PMID: 23155063
The Sequence Alignment/Map format and SAMtools.
Bioinformatics. 2009 Aug 15;25(16):2078-9 PMID: 19505943
The UCSC Genome Browser database: extensions and updates 2011.
Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23 PMID: 22086951

Article Info

Journal

Bioinformatics (Oxford, England)

Abbr.

Bioinformatics

ISSN

1367-4811

DOI

10.1093/bioinformatics/btt637

Published

2014-04-01

Epub

2013-00-13

Pages

1003-5

Language

English

Region

England

NLM ID

9808944

PMCID

PMC3967101

Subset

Grants

NHGRI NIH HHS · R01HG007354 · United States

NHGRI NIH HHS · P41 HG002371 · United States

NHGRI NIH HHS · U41 HG004568 · United States

NHGRI NIH HHS · P41HG002371 · United States

NHGRI NIH HHS · R01 HG007354 · United States

NIEHS NIH HHS · U01 ES017154 · United States

NHGRI NIH HHS · U41 HG002371 · United States

NHGRI NIH HHS · U41HG004568 · United States

NIEHS NIH HHS · U01ES017154 · United States

External Links

PubMed source DOI: 10.1093/bioinformatics/btt637 PMC Full Text View journal details

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Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

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