UCSC Archaeal Genome Browser

The UCSC Archaeal Genome Browser

The UCSC Archaeal Genome Browser is a window on the biology of more than 50 microbial species from the domain Archaea. Basic gene annotaiton is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, nucleotide and protein motifs, non-coding RNA predictions, operon predictions, and other types of bioinformatic analyses. In addition, we display available gene expression data, and soon, high-throughput RNA sequencing. Direct contributions of functional genomic data or bioinformatic analyses are welcome.

To get started, just click on a species in phylogeny tree below, select from a list of species, or choose from a pull-down menu arranged by microbial phyla (all bacteria included).

[General Help] [Extremophiles '08 Poster] Tutorial Slides: [Part 1] [Part 2] [About/Credits/Citation]

We provide a resource to closely tie research work with archaeal gene annotations. To add your publications to the genome browser, please provide the information at [Gene-Pub].

Individual Archaeal & Bacterial Genome Home Pages
(click on species name to go to genome browser home page)

Extreme Ecotypes: [H] Hyperthermophile; [T] Thermophile; [P] Psychrophile; [A] Acidophile; [K] Alkaliphile; [S] Halophile

Archaea		Bacteria
Euryarchaeota Archaeoglobi Archaeoglobus fulgidus [H] Halobacteria Haloarcula marismortui [S] Halobacterium salinarum R1 [S] Halobacterium sp [S] Haloferax volcanii [S] Haloquadratum walsbyi [S] Natronomonas pharaonis [S][K] Methanogens Methanobacteria Methanobacterium thermoautotrophicum [T] Methanobrevibacter smithii Methanosphaera stadtmanae Methanococci Methanocaldococcus jannaschii [H] Methanococcus aeolicus Methanococcus maripaludis C5 Methanococcus maripaludis C6 Methanococcus maripaludis C7 Methanococcus maripaludis S2 Methanococcus vannielii Methanomicrobiales Methanocorpusculum labreanum Z Methanoculleus marisnigri Methanoregula boonei Methanospirillum hungatei Methanosarcinales Methanococcoides burtonii [P] Methanosarcina acetivorans Methanosarcina barkeri Methanosarcina mazei Methanosaeta thermophila [T] Methanopyri Methanopyrus kandleri [H] Environmental Samples Uncultured methanogenic archaeon RC-I Thermococci Pyrococcus abyssi [H] Pyrococcus furiosus [H] Pyrococcus horikoshii [H] Thermococcus kodakaraensis [H] Thermoplasmata Ferroplasma acidarmanus [A] Picrophilus torridus [T][A] Thermoplasma acidophilum [T][A] Thermoplasma volcanium [T][A]	Crenarchaeota Desulfurococcales Aeropyrum pernix [H] Hyperthermus butylicus [H] Ignicoccus hospitalis [H] Staphylothermus marinus [H] Sulfolobales Metallosphaera sedula [T][A] Sulfolobus acidocaldarius [T][A] Sulfolobus islandicus L.S.2.15 [T][A] Sulfolobus islandicus M.14.25 [H][A] Sulfolobus islandicus M.16.27 [T][A] Sulfolobus islandicus M.16.4 [T][A] Sulfolobus islandicus Y.G.57.14 [T][A] Sulfolobus islandicus Y.N.15.51 [T][A] Sulfolobus solfataricus [H][A] Sulfolobus tokodaii [H][A] Thermoproteales Caldivirga maquilingensis [H] Pyrobaculum aerophilum [H] Pyrobaculum arsenaticum [H] Pyrobaculum calidifontis [H] Pyrobaculum islandicum [H] Thermofilum pendens [H] Thermoproteus neutrophilus [H] Marine Mesophiles Cenarchaeum symbiosum Nitrosopumilus maritimus Korarchaeota Korarchaeum cryptofilum [H] Nanoarchaeota Nanoarchaeum equitans [H]	Extremophiles Aquifex aeolicus [H] Bacillus halodurans [S][K] Carboxydothermus hydrogenoformans Z-2901 [T] Desulfotalea psychrophila LSv54 [P] Salinibacter ruber DSM 13855 [S] Thermoanaerobacter tengcongensis [T] Thermobifida fusca YX [T] Thermotoga maritima [H] Thermus thermophilus HB27 [T] Thermus thermophilus HB8 [T] Thermosynechococcus elongatus [T] Deinococcus radiodurans Selected Metal-reducing Bacteria Geobacillus kaustophilus HTA426 Geobacter metallireducens GS-15 Geobacter sulfurreducens Shewanella oneidensis Selected Model Bacteria Bacillus subtilis Escherichia coli CFT073 Escherichia coli K12 Escherichia coli O157H7 Salmonella enterica Choleraesuis Salmonella typhi Selected Pathologens Campylobacter jejuni Helicobacter hepaticus Helicobacter pylori 26695 Helicobacter pylori J99 Vibrio cholerae O1 El Tor Vibrio fischeri ES114 Vibrio parahaemolyticus Vibrio vulnificus CMCP6 Vibrio vulnificus YJ016 Vibrio cholerae O395

About

The Achaeal Genome Browsers at UCSC were developed by members of the Lowe Lab, with significant support from the UCSC Human Genome Browser group. The Archaeal Browsers are run by a slightly modified version of the UCSC Human Genome Browser system. All queries, bug reports, content corrections, suggested improvements, and new track data submissions should be sent to Todd Lowe (lowe @soe.ucsc.edu).

Additional extremophile and other model bacteria are available from main genome menu. New species are added as they become public, and upon request.

Citation and Funding Support

If you use the browser in your published research, please cite our publication in the Nucleic Acids Research Database Issue. Citations and positive feedback will help us continue development and future support of this community resource. Current support for this project is generously provided by the National Science Foundation (Award #0641061).