Figure 2

Using the geometric criterion (Eq. 4) exclusively to detect the query in PDB25. The histogram shows the cumulative percentage of cases for which the self-match score is found within the top percentage shown on the x-axis. Full line: using δ = 0.1, and dashed line: using δ = 0.3. For both choices of δ self match is always the highest on the list if the sequential ordering (Eq. 6) is used as an additional requirement (i.e. the graph looks the same as δ = 0.1 case shown in red here). Thus in a general comparison strategy one cannot rely on matching directions alone - additional constraints are needed to reduce the number of false positives.