Multidimensional whole genome synteny

A popular means to compare whole genomes is the use of Syntenic dotplots. These dotplots reveal regions of the genomes that are related through common ancestry -- either through the divergence of lineages/species or through intra-genomic duplications. CoGe makes the generation of these available through its tool SynMap as well as providing the means to add additional information about the divergence age of syntenic gene pairs to the dots in the dotplot.

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	Syntenic dotplot of the maize genome versus the sorghum genome. Syntenic dots are colored by Ks values which is a proxy for their divergence age. Note that there are two major colors -- purple and cyan. The purple dots reflect younger gene pairs and cyan dots reflect older gene pairs. File:File:Master 16904 93.CDS-CDS.last.tdd10.cs0.filtered.dag.all.go D20 g10 A5.aligncoords.gcoords ct0.w1000.gene.s.ks.sr.cs1.csoN.log.nsd.hist.png 200px