The synteny connections are based on a combination of explicit orthology assertions from Xenbase.org, drawn from expert curation and NCBI's Ortholog and Homologene data sets, and symbol-based matching using the gene symbols from the GFF files. A window of genes 5 upstream and 5 downstream from the gene of interest are extracted from the source GFFs for each species and stored in the CMAP format. An optimization step is then used to maximize the longest common subsequence (LCS) between all of the genes in the window for each species.
Optimization is performed by iteratively inverting the gene orders for each species and recalculating the overall LCS value across species. The optimized set is the orientation of all genomes giving the highest overall LCS. These optimized orientations are then used for rendering the images.
Caveats:
Not every gene in the Xenopus genomes is represented here, only protein coding genes with meaningful gene symbols, i.e. not LOC######, and identified orthologs. LOC genes will show up in simple synteny figures but cannot themselves be searched for. If you cannot find a specific gene of interest we suggest using other genes from the equivalent locus in another species to explore the region, if possible.
The original SimpleSynteny tool is described in Veltri, D., Malapi-Wight, M. and Crouch J.A. SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species. Nucleic Acids Res. 44(W1):W41-W45, 2016. doi:10.1093/nar/gkw330