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 and must be entered correctly for the query genome. Here
is the formatting for each species (note that even correct capitalization
is important):
| Genome |
Typical
scaffold name |
| Tetraodon nigroviridis |
numeral,
X, or Y, for chromosome designation, MT for mtDNA, "un_random"
or "<numeral>_random" |
| Xenopus tropicalis |
scaffold_<numeral> |
| Xiphophorus maculatus |
contig<numeral> |
| Ciona intestinalis |
<numeral>p
or <numeral>q for chromosome designation, scaffold_<numeral> |
| Danio rerio |
numeral for
chromosome designation, MT for mtDNA, Zv8_NA<numeral>,
Zv8_scaffold<numeral> |
| Gallus gallus |
numeral, W,
or Z for chromosome designation, W_random, Z_random, E22C19W28_E50C23,
E22C19W28_E50C23_random, E64, E64_random, MT for mtDNA |
Gastersteus aculatus
|
Scaffold_<numeral>,
group<roman numeral>, MT for mtDNA |
Homo sapiens
|
numeral, X,
or Y, for chromosome designation, MT for mtDNA |
Monodelphis domestica
|
numeral, X,
or Y, for chromosome designation, "Un", MT for mtDNA |
Mus musculus
|
numeral, X,
or Y, for chromosome designation, NT<6 numerals>, MT
for mtDNA |
Oryzias latipes
|
numeral for
chromosome designation, ultracontig<numeral>, scaffold<numeral>
|
Strongylocentrotus purpuratus
|
Not available
at this time. |
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).
In some cases as
well, alternative splicing variants may appear as though they are
independent loci, so caution is urged to verify conclusions about
individual gene family evolution.
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.
|
