Alignment Scoring Algorithm

library(fsmc)

The identity matrix is given as the non-redundant count of reactions in the given level of the alignment over the count of all reactions in the set of consortia.

BM = binary matrix representing all edges in the set of consortia

$$\sum \text{BM} - \left( \sum_{i < j} A^{(2)}(i,j) + A^{(N)} \right) - \left( \sum_{i < j < k} A^{(3)}(i,j,k) + A^{(N)} \right)$$

• How does this score compare against the tanimoto coefficient?