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Partnering for Discovery

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):

Typical scaffold name
Tetraodon nigroviridis
numeral, X, or Y, for chromosome designation, MT for mtDNA, "un_random" or "<numeral>_random"
Xenopus tropicalis
Xiphophorus maculatus
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.