Name URL Description
Ensembl http://www.ensembl.org/ Major species with completed genome sequences providing lineage-specific web portals for vertebrates, metazoa, plants, fungi, protists and bacteria.
UCSC http://genome.ucsc.edu/cgi-bin/hgGateway Major species with completed genome sequences including vertebrates, deuterostomes, insects and nematodes. No plant species.
Map Viewer http://www.ncbi.nlm.nih.gov/mapview/ Major species with completed genome sequences including vertebrates, invertebrates, protozoa, plants and fungi, as well as dozens of uncompleted plant genomes.
Phytozome http://www.phytozome.net/cgi-bin/gbrowse/ Major plant species with completed and ongoing genome sequences including monocots, dicots, fern, moss and green algae, with VISTA alignments.
Gramene http://www.gramene.org/genome_browser/ Major plant species with completed genome sequences including monocots, dicots, fern, moss and green algae, and the short arm of chromosome 3 of several wild rice species.
VISTA http://pipeline.lbl.gov/cgi-bin/gateway2/ Whole genome alignment presentation, including vertebrates, insects, nematodes, deuterostomes, plants, fungi, alga, annelids, stramenopiles and metazoa.
Genome Projector http://www.g-language.org/g3/ Several hundreds of bacteria genomes with circular or linear maps.
Annmap http://annmap.picr.man.ac.uk/ A genome browser that includes mappings between genomic features and Affymetrix microarrays for human, mouse, rat and yeast.

Table 2:
List of some web-based species-specific genome browsers

Name URL Species
Animals
    MGI http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/ Mus musculus (Mouse)
    RGD http://rgd.mcw.edu/fgb2/gbrowse/ Rattus norvegicus (Rat)
    Xenbase http://www.xenbase.org/fgb2/gbrowse/ Xenopus tropicalis (Frog)
    ZFIN http://zfin.org/cgi-perl/gbrowse/ Danio rareo (Zebrafish)
    Flybase http://flybase.org/cgi-bin/gbrowse/ Drosophila (Fruit fly)
    BeetleBase http://beetlebase.org/cgi-bin/gbrowse/ Tribolium Castaneum (Beetle)
    AphidBase http://isyip.genouest.org/cgi-bin/gb2/gbrowse/ Acyrthosiphon pisum (Aphid)
    wFleaBase http://wfleabase.org/gbrowse/ Daphnia (Water flea)
    Wormbase http://www.wormbase.org/db/gb2/gbrowse/ Caenorhaditus elegans (Worm)
Plants
    TAIR http://www.arabidopsis.org/browse/ Arabidopsis thaliana (Wall cress)
    BRAD http://brassicadb.org/cgi-bin/gbrowse/ Brassica rapa (Brassica)
    SGN http://solgenomics.net/gbrowse/bin/gbrowse/ Solanum pimpinellifolium (Tomato)
    Popgenie http://www.popgenie.org/tool/gbrowse/ Populus trichocarpa (Populus)
    Rice Genome http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/ Oryza sativa japonica (Rice)
    Rice-Map http://www.ricemap.org/ Oryza sativa japonica/indica (Rice)
    MaizeDB http://gbrowse.maizegdb.org/ Zea mays (Maize)
Microbes
    dictyBase http://dictybase.org/db/cgi-bin/ggb/gbrowse/ Dictyostelium discoideum (Dictyostelid)
    SGD http://browse.yeastgenome.org/ Saccharomyces cerevisiae (Yeast)
    ParameciumDB http://paramecium.cgm.cnrs-gif.fr/cgi-bin/gbrowse2/ Paramecium tetraurelia

Table 3:
List of web-based genome browser frameworks

Name URL Description
General viewer
    Ensembl http://www.ensembl.org/ An extensible software architecture with powerful API support.
    UCSC http://genome.ucsc.edu/ A freely downloadable package for local browser installation.
    GBrowse http://gmod.org/wiki/GBrowse The most popular genome viewer for multiple genome annotation visualization, especially for model organism database projects.
    JBrowse http://jbrowse.org/ A JavaScript-based genome browser, providing Google-map like new browsing experience.
    ABrowse http://www.abrowse.org/ A new-generation customizable genome browser framework.
    Anno-J http://www.annoj.org/ An interactive application designed for visualizing genome annotation data and deep sequencing data.
    SViewer http://www.ncbi.nlm.nih.gov/projects/sviewer/ NCBI’s new Sequence Viewer.
Synteny viewer
    GBrowse_syn http://gmod.org/wiki/GBrowse_syn A GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared with two or more additional species.
    SynBrowse http://www.synbrowse.org/ A generic sequence comparison tool for visualizing genome alignments both within and between species.
    SynView http://www.eupathdb.org/apps/SynView/ A light-weight, interactive and highly customizable comparative genomic visualization tool based on GBrowse.
    Sybil http://sybil.sourceforge.net/ A web-based software package for comparative genomics.
Next generation sequencing data viewer
    LookSeq http://www.sanger.ac.uk/resources/software/lookseq/ A web-based application for alignment visualization, browsing and analysis of genome sequence data including short reads generated by next-generation sequencing.