Table 1 compares the relative performance of our parsimony-based approach and the probabilistic method described by Pinney et al. [ 18] Our results were generated using a ratio of 11.4 : 1 for the cost of interaction creation to interaction deletion (the same ratio as was used in the probabilistic method).
Cost of interaction between an accessible region r i and two other accessible regions s k and s j is defined as where s k s j is the concatenation of two subsequences, and E u (s k, s j ) = (-RT) ln(ℙ u [ s k ], u [ s j ])).
This is consistent with the idea of a higher pre-formed conformation for binding of peptide K156 compared with peptide HTHi that lowers the entropy cost of interaction of the former.
Similarly the cost of interaction between two accessible regions from R and one accessible region from S is defined.
Also we need O(n'.m'.w) time and O w) space to compute the cost of interaction for every pair of accessible regions.
Also the cost of interaction where minimum free energy MFE(r i, s k s j ) is used instead of ensemble energy E I (r i, s k s j ) can be defined in a similar way.
Thus, functional co-adaptation and/or parasitic co-evolution would not apply in tropical regions since avoidance mechanisms are selected only if the cost of avoidance is lower than the cost of interaction [ 72].
We have The cost of interaction between two accessible regions r i and s j, C(r i, s j ), is the sum of the following terms: (i) E u (r i ), (ii) E u (s j ), and (iii) E I (r i, s j ) or MFE(r i, s j ).
