Relaxation filter

If a query sequence has four motifs (A, B, C and D), there are six motif-pair spacings possible (AB, AC, AD, BC, BD and CD). Similarly, within the .hit. if all the 4 motifs (a, b, c and d) are present there will be six different motif spacers (like ab, ac, ad, bc, bd and cd). For each equivalent spacing between query and hit (like AB and ab), a relaxation filter is applied to make the motif based search more sensitive. Our benchmarking studies indicated that 30% relaxation of equivalent motif spacing provide optimal results with high specificity. So, if the spacing between query and hit passes the relaxation filter, we select it as a matched-motif pair (AB and ab).