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. | |||
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-mirror.cshl.edu/ Cold Spring Harbor Laboratory]. CSHL, NY | |||
* [http://genome-mirror. | |||
* [http://genome-mirror.moma.ki.au.dk/ 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). | 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 === | ||
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.
- Cold Spring Harbor Laboratory. CSHL, NY
- 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).
- Ververt monkey at McGill
- Cannabis sativa at U Toronto
- Aedes aegypti and two other mosquitoes at CalTech
- Penn State has some personal human genomes not at UCSC
- 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)
- Sticklebrowser at Stanford.
- Heliconius butterfly at Cornell (butterflygenome.org).
- Puerto Rican parrot at WashU (+ alternate assemblies of Drosophila spp.).
- Pleurobrachia bachei ctenophore from Whitney Laboratory for Marine Bioscience, St. Augustine, FL.
- 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.
- Xenopus laevis Frog at Medical Research Council, UK.
- 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
- 1000 Genomes A Deep Catalog of Human Genetic Variation
- NONCODE genome browser. UCSC browser with special tracks for non-coding annotations.
- Jim Watson genome browser at CSHL
- Craig Venter genome data release
- dbRIP - Retroposon Insertions Roswell Park Cancer Institute, MD
- Vista Lawrence Berkeley Lab, CA
- GARFIELD cat genome browser, Federick, MD
- C. intestinalis: UCSC-based, Gbrowse
- The JGI-browser for various species: Fugu, C.intestinalis, waterflea, sponge, amphioxus, snail, hydra, etc...
- Bio2Rdf Semantic web atlas of postgenomic knowledge about human and mouse
- Aedes aegypti mosquito
- Silkworm Bombyx mori, China
- NRSP-8 National Animal Genome Research Program - Bioinformatics Coordination Program
Plant Browsers
- EnsemblPlants incl. Arabidopsis, rice, corn, tomato, soybean, Physcomitrella
- Arabidopsis Thaliana TAIR-10 UCSC public hub (see also: list of public hubs)
- Brassica rapa UCSC public hub (see also: list of public hubs)
- Ricinus communis UCSC public hub (see also: list of public hubs)
- Arabidopsis genome browser at UCLA
- Arabidopsis genome browser at Dartmouth.
- Arabidopsis arabidopsis.info Ensembl-based genome browser
- UNLV Las Vegas Genome Browser hosting: Arabidopsis, rice, sorghum and soybean, as well as D. melanogaster
- gramene.org many rice genomes and other grasses
- RICE FPC Genome Browser from the Arizona Genomics Institute (AGI)
- Zea mays Maize Genome Sequencing Project
Fungi/Yeast Browsers
- Saccharomyces cerevisiae database and genome browser from SGD/Stanford University
- S. pombe (fission yeast) at NCI, NIH
Other
- Archaea browser from the Lowe Lab at UCSC
- Paramecium tetraurelia Genoscope, France
- JPGV Jena Prokaryotic Genome Browser
