MicrobesOnline provides a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi, thousands of expression microarrays from diverse organisms, and fitness data for 4 organisms with over 2,000 comparisons.
To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved.
MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources, including Genome-Linked Application for Metabolic Maps (GLAMM) - a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks and investigating the construction of novel, transgenic pathways.
The genome selector lets you choose which genomes you are interested in. Type the first few letters of the genome name (e.g., "esc" for Escherichia coli) to get a short list of candidates, and then double-click on the ones you want. Your current selection is shown in the middle box.
The genome selector also lets you choose phylogenetic groups of genomes. For example, if you want to search for the presence of a specific capability across the Gammaproteobacteria, type "gamm", double-click on "Gammaproteobacteria", and then type in your keyword at the right. You can search all available genomes by selecting "cellular organisms". Other high-level groups include "Bacteria" and "Archaea".
When your list of genomes is finished push the "Add present" or "Add absent" to set up if you are looking genes that are present or absent from these phyla.