In the case of Oomycetes there is an theory of the existence of two speed genome. That there is two sets of genes which undergo different evolutionary rate and that they also differ based on their location in the genome. With respect to 5' and 3' flanking region of non overlapping genes one set have smaller values and one set has larger values that is they are dispersed in the genome compared to the first set. This approach was followed because the Oomycetes genome is tough to assemble into chromosome level because of the heterogenicity of the samples from mycelia.
Here we only consider Phytophthora from Oomycetes.
STEP 1;
Canculating Flnaking intergenic regions for genes. Remove genes located in ends of the scaffold or chromosome Overlapping genes have 0 length on that flank. Gene location will be considered irrspective of direction of transcription.