Other genome browsers: Difference between revisions

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== Official UCSC Genome mirror site ==
== Official UCSC Genome mirror site ==


* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.
* [http://genome-euro.ucsc.edu/ euronode] Bielefeld, Germany.
* [http://genome-asia.ucsc.edu/ asianode] RIKEN.  Yokahama, Japan.


This mirror is maintained by the Browser staff.
These mirrors are maintained by the Browser staff.
 


== UCSC Genome mirror sites ==
== UCSC Genome mirror sites ==
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These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.
These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.


* [http://genome.hmgc.mcw.edu/ Medical College of Wisconsin] Milwaukee, WI
* [http://genome-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY


* [http://genome-mirror.bscb.cornell.edu/ Cornell University] Ithaca, NY
* [http://genome-mirror.moma.ki.au.dk/ Aarhus University]. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark


* [http://moma.ki.au.dk/genome-mirror/ Aarhus University] The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark
== Other locations hosting UCSC Genome Browsers ==
 
 
== Locations using UCSC software on other organisms (or people) or additional content on our organisms ==
Note that not all of these sites are updating their software to the latest versions.  To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).
Note that not all of these sites are updating their software to the latest versions.  To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).


* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill
* [http://www.genomequebec.mcgill.ca/compgen/browser-VPR/cgi-bin/hgGateway Ververt monkey] at McGill


* [http://genome.ccbr.utoronto.ca/ Cannabis sativa]  at U Toronto
* [http://genome.ccbr.utoronto.ca/ <i>Cannabis sativa</i>]  at U Toronto


* [http://aedes.caltech.edu/cgi-bin/hgGateway Aedes aegypti] and two other mosquitoes at CalTech
* [http://aedes.caltech.edu/cgi-bin/hgGateway <i>Aedes aegypti</i>] and two other mosquitoes at CalTech


* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC
* Penn State has some [http://main.genome-browser.bx.psu.edu personal human genomes] not at UCSC


* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, C. intestinalis and other orgs.
* [http://genome.smith.man.ac.uk Manchester, UK] has some local content on mouse, <i>C. intestinalis</i> and other orgs. (seems to have been retired or moved)


* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly contained in the Track Data Hubs at UCSC.
* [http://epigenome.wustl.edu/ Epigenomics] Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.


* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting D. melanogaster and some plants
* [http://shenlab.sols.unlv.edu/cgi-bin/hgGateway UNLV Las Vegas] Genome Browser hosting <i>D. melanogaster</i> and some plants (including rice, sorghum, <i>Arabidopsis</i>)


* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.
* [http://sticklebrowser.stanford.edu/ Sticklebrowser] at Stanford.


* [http://cbsugb.tc.cornell.edu/cgi-bin/hgGateway <i>Heliconius</i> butterfly] at Cornell ([http://butterflygenome.org/node/2 butterflygenome.org]).
* [http://gander.wustl.edu/cgi-bin/hgGateway?db=amaVit1 Puerto Rican parrot] at [http://gander.wustl.edu/ WashU] (+ alternate assemblies of <i>Drosophila</i> spp.).
* [http://128.227.123.35:8889/cgi-bin/hgGateway?clade=other&org=Pleurobrachia+bachei&db=0 <i>Pleurobrachia bachei </i> ctenophore] from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.
* [http://gwips.ucc.ie/cgi-bin/hgTrackUi?hgsid=10019&c=chr20&g=Global GWIPS-viz] Genome-Wide Information on Protein Synthesis, including <I>Arabidopsis</I>, Trypanosome, herpes virus, phage lambda and others.  University College, Cork, Ireland.
* [http://gander.wustl.edu/cgi-bin/hgGateway?clade=vertebrate&org=A.+vittata&db=0 Puerto Rican Parrot] as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.
* [http://genomaize.org/cgi-bin/hgGateway Maize] at Florida State University.
* [http://genomes.nimr.mrc.ac.uk/cgi-bin/hgGateway Xenopus laevis] Frog at Medical Research Council, UK.
* [http://old-gander.wustl.edu/gonramphubs/index.html various hubs] At WashU for: <I>Amazona vittata</I> (Puerto Rican Parrot), <I>Chlamydomonas reinhardtii</I> (single-celled alga), <I>Kryptolebias marmoratus</I>, <I>Sebastes rubrivinctus</I>, <I>Xenopus laevis</I> (frog commonly used used in research)
* [http://genomes.mcdb.ucla.edu/cgi-bin/hgGateway plants].  Oak, Rice, <I>Arabidopsis</I>, <i>Chlamydomonas</i>, <i>Volvox</i>, soybean, diatom, <i>Chromochlorus</i> algae, prune, some fungi, bacteria.  At UCLA.
* [http://em-x1.gurdon.cam.ac.uk/cgi-bin/hgGateway vertebrates].  Various new fish.  At Cambridge University, UK.
* [http://rohsdb.cmb.usc.edu/index.html DNA Shape] at University of Southern California.  G-shape.  Genome Browser Database for Shape Annotations.  Many genomes.  Some plants.
* [http://genome.genetics.rutgers.edu/ Rutgers].  G-shape.  Genome Browserfor several genomes.  Some plants (incl. millet, switchgrass, soybean, rice), insects.


== Browsers Using Non-UCSC Software==
== Browsers Using Non-UCSC Software==


The UCSC Genome Browser is primarily funded to host vertebrate genomes.  If you are looking for a genome browser that UCSC does not host, it may be available from another source.  These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.
The UCSC Genome Browser is primarily funded to host vertebrate genomes.  However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the [http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly Assembly Hub] mechanism.
 
If you are looking for a genome browser that UCSC does not host, it may be available from another source.  These browsers are not affiliated with the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser] and any questions regarding them should be directed to their hosts.


=== Animal Browsers ===
=== Animal Browsers ===
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* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella
* [http://plants.ensembl.org/index.html EnsemblPlants] incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella


* Assembly hub including A. thaliana, B. rapa, and R. communis at UCSC. It can be found in Genome Browser's [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs], under the name 'Plants'.
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=araTha1.hub Arabidopsis Thaliana] TAIR-10 UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=braRap1.hub Brassica rapa] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])
 
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=hiram&hgS_otherUserSessionName=ricCom1.hub Ricinus communis] UCSC public hub (see also: [http://genome.ucsc.edu/cgi-bin/hgHubConnect list of public hubs])


* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA
* [http://epigenomics.mcdb.ucla.edu/ Arabidopsis] genome browser at UCLA

Latest revision as of 17:51, 14 February 2018

Official UCSC Genome mirror site

These mirrors are maintained by the Browser staff.

UCSC Genome mirror sites

These mirrors are not populated nor maintained by UCSC. Any questions regarding them should be directed towards their host institution/organization.

  • Aarhus University. The Department of Molecular Medicine (MOMA) at Aarhus University, Denmark

Other locations hosting UCSC Genome Browsers

Note that not all of these sites are updating their software to the latest versions. To learn what version is being used, look at the v### number at the top of the hgTracks page ([host]/cgi-bin/hgTracks).

  • Manchester, UK has some local content on mouse, C. intestinalis and other orgs. (seems to have been retired or moved)
  • Epigenomics Epigenomics Roadmap mirror at Washington University, St. Louis has content not on the main UCSC Browser, but mostly also contained in the Track Data Hubs at UCSC.
  • UNLV Las Vegas Genome Browser hosting D. melanogaster and some plants (including rice, sorghum, Arabidopsis)
  • GWIPS-viz Genome-Wide Information on Protein Synthesis, including Arabidopsis, Trypanosome, herpes virus, phage lambda and others. University College, Cork, Ireland.
  • Puerto Rican Parrot as well as chicken with some bird comparative genomics and Drosophila spp.. Genomics Education Partnership, Washington University, St. Louis.
  • Maize at Florida State University.
  • various hubs At WashU for: Amazona vittata (Puerto Rican Parrot), Chlamydomonas reinhardtii (single-celled alga), Kryptolebias marmoratus, Sebastes rubrivinctus, Xenopus laevis (frog commonly used used in research)
  • plants. Oak, Rice, Arabidopsis, Chlamydomonas, Volvox, soybean, diatom, Chromochlorus algae, prune, some fungi, bacteria. At UCLA.
  • vertebrates. Various new fish. At Cambridge University, UK.
  • DNA Shape at University of Southern California. G-shape. Genome Browser Database for Shape Annotations. Many genomes. Some plants.
  • Rutgers. G-shape. Genome Browserfor several genomes. Some plants (incl. millet, switchgrass, soybean, rice), insects.

Browsers Using Non-UCSC Software

The UCSC Genome Browser is primarily funded to host vertebrate genomes. However, you can load your own assemblies onto the UCSC site without intervention by UCSC using the Assembly Hub mechanism.

If you are looking for a genome browser that UCSC does not host, it may be available from another source. These browsers are not affiliated with the UCSC Genome Browser and any questions regarding them should be directed to their hosts.

Animal Browsers

  • NONCODE genome browser. UCSC browser with special tracks for non-coding annotations.
  • Vista Lawrence Berkeley Lab, CA
  • GARFIELD cat genome browser, Federick, MD
  • Bio2Rdf Semantic web atlas of postgenomic knowledge about human and mouse
  • NRSP-8 National Animal Genome Research Program - Bioinformatics Coordination Program

Plant Browsers

  • EnsemblPlants incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella
  • Arabidopsis arabidopsis.info Ensembl-based genome browser
  • Zea mays Maize Genome Sequencing Project

Fungi/Yeast Browsers

Other

  • JPGV Jena Prokaryotic Genome Browser

See Also

Related Wikis

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