Figure 2

Performance on RCPs. The methodology of CPSARST is not only applicable to structurally meaningful RM strings but also to amino acid sequences. Random CP followed by various degrees of random substitutions, insertions and deletions were performed on 100 amino acid sequences. The performance of CPSARST was monitored by (a) the percentage of cases in which the exact permutation site was retrieved, and (b) the percentage distance of the retrieved permutation site to the exact one. The dashed line in (a) represents a 50% cut, above which more than half of the permutation sites were exactly predicted. When it only depends on amino acid sequences to detect CP, CPSARST can be reliable even if the identity is as low as 20%. UFAU stands for the CP-detecting method developed by Uliel et al. [38].