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         Explanation of the "Synteny Viewer Page"    
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Explanation of the "Synteny Viewer Page"

Select a query genome, a scaffold, and a span of gene position numbers on that scaffold. In most cases, the default values for the maximum gene distance to display as syntenic (30 genes) and the minimum distance to flip the segment in orientation (0.5) are acceptable, but these can be changed if it clarifies a presentation. The size of the window for the display can be specified. Choose one or more genomes to compare and click “submit”. After the display refreshes, these parameters can be reset, and there are controls for moving up or down the query scaffold and for zooming in and out.

Note that the naming conventions for scaffolds vary among the different organisms. For illustration, here is the name of one scaffold for each species (note that even correct capitalization is important):

Typical scaffold name
  Hyaloperonospora arabidopsidis
  Phytophthora infestans
  Phytophthora ramorum
  Phytophthora sojae
  Phaeodactylum tricornutum
  Pythium ultimum
  Thalassiosira pseudonana

Each query gene in the specified span finds the gene of reciprocally shortest distance to a gene in the target genome. These are displayed here only if they have been united in a phylogenetic cluster during the analysis. These pairs may be orthologs, but if there are multiple in-paralogs, this will show only the one that has the shortest distance (i.e., is the most slowly evolving).

The presentation can be reoriented by clicking on the scaffold name to place that genome in the center. Mousing over each gene gives some details in a pop-up box. Clicking on the gene calls up the Details Page.

Connecting lines in red indicate that the gene pair is inverted relative to one another. Genes are in gray if there is no homolog identified.