There are several ways to determine whether your protein/gene of interest is in a region that is syntenic to other organisms in the ERGO database.

First, bring up the protein page for the protein you are interested in.

The first way to look at chromosome synteny is through the "Pinned Regions" tool, which can be found in the "Examine" menu.

After you click the link, you will see an image that looks something like this:

Where the reference protein is always the central red proteins and the remaining proteins are color coded so that all proteins that are considered "pinned orthologs" of each other are painted with the same color.

The second way to look at synteny across one or more organisms is through the "Contig Regions" tool, which can be found in the "Examine Checked" menu box on the bottom left side of the protein page:

Select the orthologs that you want to compare regions with and then click the "Contig Regions" link to bring up a regional alignment that looks something like this"

This display includes a 10 kb region upstream and downstream from the reference ORF for all the proteins that you selected. Homologous ORFs are colored with the same color across all regions. You can ask for the ORFs to be color-coded based on orthology or simple sequence similarity. Just use the drop down menu to select the mechanism by which you want to color code and type the similarity threshhold into the "cutoff" box.

You can find the GenomeAlign alignments available to you by going to the green "Data" drop down menu and selecting "GenomeAlign".

Selecting GenomeAlign from the Data Drop Down Menu

After that, you can find the data you have access to in one of two ways.

The GenomeAlign Menu Page

BLAST Menu Driven
You can follow the menu driven system that will allow you to set the BLAST score cutoff and length of BLAST hit that you want to use to compare your two genomes of interest. After you choose your BLAST thresholds and click the "Select BLAST cutoffs" button, you can select the Query organism from a drop down menu (the query organism is always the organism you are "BLASTing into" another organism) and then you can select the Target organism (the organism you are "BLASTing against"). The Target organism set will be smaller than the Query organism set since the data is pre-calculated and ERGO will filter the Target organism set based on the data available for the Query organism you selected.

Display All Available BLAST Runs
You can click the link "Display all available BLAST runs" (above the BLAST menu box) which will pull up a table of query and target organisms. Clicking on the "Show" link in the far right column next to any query/target pair will pull up the graphical display using the default BLAST settings (the default BLAST settings are the same as what you see when you first see the BLAST menu -- 1e-20 score cutoff and 200bp hit length cutoff.

Selecting Data from the List of Available BLAST Runs

Either of these entry points will take you to the graphical GenomeAlign view.

GenomeAlign Viewer Page

You can mouse over any feature in either the query or target genome for more information about the feature and the alignment. For more information about the color coding and tool tip displays once you have the GenomeAlign page, please click on the blue "?" box in the "Alignment of BLAST hits from:" box at the top of the page to bring up the Help information.

GenomeWalk is a tool (found in the "Tools" menu) that allows you to compare the predicted proteomes of two or more genomes. We've created a detailed tutorial explaining how to create the comparison genome sets and look at the results.

The document is in PDF format. You will need a PDF file reader such as Adobe Acrobat Reader in order to open the document.

GenomeWalk Tutorial