Figure 3
Example of a merge between two diagonals. Two chromosomes, c a of n a = 11 tbs and c b of n b = 8 tbs, are compared. The number in each tb is its size, arrows indicate tbs orientations and if a tb is represented as a rectangle it means that it has an unknown orientation. The MHP contains n a b = 6 hps. During step 2, PhylDiag finds two strict backslash diagonals and 2 single hps. Each strict diagonal contains 2 hps. If g a p m a x = 4, during the diagonal merging process, diagonals separated by a distance of 2 to g a p m a x +1=5 are merged. Consider that the user chooses the DPD metric, when reaching a distance of 5, two possible fusions are theoretically possible, one between the two extremities of the strict backslash diagonals and another fusion between the single hp (coordinates [ 2,6]) and the extremity (coordinates [5,5]) of the leftmost strict diagonal. However since the sign of the single hp is not consistent with the diagonal type of the left-most diagonal, the second fusion is not performed. Around the resulting consistent diagonal (in red) three windows are drawn: W a (purple) on c a contains 6 tbs and W b (green) on c b contains 4 tbs, and at last the window W a b (pink) contains 6 × 4 cells and 4 hps. These windows are useful in section ‘Step 4: Statistical validation of consistent diagonals as synteny blocks’ for the p-value calculation.