Figure 4

Allen's set of relations and their extension for the expression of KS patterns. I and J are two features (intervals) defined by their type and the position of their beginning and end on the sequence. (a) Allen's original relations. (b) extensions of the Allen's set of relations to take into account two specificities of intervals over DNA sequences. same-strand (I, J) holds if I and J are on the same strand; diff-strand (I, J) holds if I and J are on opposite strands. same-phase (I, J) holds if I and J are in the same phase (i.e. they are on the same strand and they are separated by a multiple of three bases); diff-phase (I, J) holds if I and J are on different phases.