Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Figure 10
Calculating Minimum Syntenic Distance for Orthologues
The minimum syntenic distance is the smallest difference in gene order between neighbours of its orthologues in the other species. Starting from human gene H1, the chromosomal location of its dog orthologue D1 is noted (step 1). The flanking genes (within a window of 20 sets of orthologues) are searched for the nearest neighbouring human gene with an orthologue on the same chromosome as D1. Thus, the immediate neighbour to the right of H1 can be ignored because it does not have an orthologue on the same chromosome as D1 (step 2). The subsequent gene H2 has a dog orthologue (step 3) D2 on the same chromosome as D1. The syntenic distance for gene H1 in the downstream direction is calculated to be four genes, by counting the number of intervening genes (using Ensembl gene loci) between D1 and D2 (step 4). Upstream of H1 and D1, however, no genes have been inserted after the next orthologous genes H3 and D3. The minimum syntenic distance for H1 is thus 1.