Other genome browsers

From genomewiki
Jump to: navigation, search

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