Protein Q and any protein S retrieved by iSARST in the hit list were defined as a neighboring structural pair (NS pair).
The path connective value (PCV) is the product of CVs of all neighboring pairs along the path P (3).
A gene pair, g0, g1 ∈ G, is a neighboring gene pair if Dist g0, g1) ≤ MAX_ GAP, and an OG pair, F0, F1 ∈ F, is a neighboring OG pair if there exists a neighboring gene pair g0, g1 such that g0 ∈ F0, g1 ∈ F1.
For the sake of clarity, the problem mentioned above is illustrated in Figure 1 in the form of a graph, where connectivity of each neighboring pair is shown with the help of a solid line.
In our analysis, we explicitly ignored recombination and therefore we used the number of same-strand neighboring gene pairs, rather than the number of genes, because a neighboring gene pair located on opposite strands cannot become overlapping on the same strand as a result of point mutation.
We define a depth discontinuity pixel (DDP) to be a neighboring pixel pair {f o,p o} positioned in the original view as shown in Fig. 4 that satisfy the following conditions: text{DDP} = left{mathbf{f}_{mathrm{o}}, mathbf{p}_{mathrm{o}}right}; left| mathbf{d}_{mathrm{v}} right|_{2} > eta, (1).
First, let us define a neighboring OG pair.
Assume that the common ancestor contained a neighboring gene pair A,B together with a cis-regulatory region c that affects both genes (c-A-B).
A more recent study showed that there is a difference from a random null model in the fraction of gene pairs in the same GO-slim process only for neighboring pairs with a high level of coexpression (r > 0.4) [ 12].
This resulted in a limited set of 16 neighboring pairs of genes that potentially correspond to T. spiralis operons; however, further characterization of these candidate operons was not undertaken.
