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):
|
Genome |
Typical
scaffold name |
|
Hyaloperonospora
arabidopsidis |
Scaffold_1 |
|
Phytophthora infestans |
supercont1.1 |
|
Phytophthora ramorum |
scaffold_1 |
|
Phytophthora sojae |
scaffold_1 |
|
Phaeodactylum tricornutum |
chr_1 |
|
Pythium ultimum |
scf1117875581239 |
|
Thalassiosira pseudonana
|
chr_1 |
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.
|