UCSC Microbial Genome Browser
Help FAQ Tutorial Credits Lowe Lab
Enter Partial Name to Select Genome

(Examples: "Pyro", "furi")

The UCSC Microbial Genome Browser is a window on the biology of more than 300 microbial species from Bacteria and Archaea domains. 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.

petri dish

Available genomes arranged in phyla

Archaea Bacteria
Crenarchaeota Actinobacteria
Euryarchaeota Aquificae
Nanoarchaeota Bacteroidetes
Korarchaeota Cyanobacteria
Archaeal viruses Firmicutes

Selected genomes that may be of interest

Archaea Bacteria
Aeropyrum pernix Aquifex aeolicus
Pyrobaculum aerophilum Gloeobacter violaceus
Sulfolobus solfataricus Bacillus subtilis
Halobacterium sp. NRC-1 Clostridium difficile
Methanococcus jannaschii Staphylococcus aureus Mu50
Methanococcus maripaludis Helicobacter pylori J99
Methanopyrus kandleri Escherichia coli K12
Pyrococcus furiosus Pseudomonas aeruginosa
Thermoplasma volcanium Thermus thermophilus HB27




The following poster and tutorials provide an overview on how to use different features in the genome browser.

Extremophiles '08 Poster
Tutorial Part 1
Tutorial Part 2


The Microbial Genome Browser at UCSC was developed by members of the Lowe Lab, with significant support from the UCSC Genome Browser group. The Microbial Browser is run by a slightly modified version of the UCSC 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).

New species are added as they become public, and upon request.

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).