This chapter has introduced a new method of efficiently finding optimal homomorphisms from a directed graph with a restricted cyclic structure to an arbitrary network using enzyme matching cost based on EC notation. The proposed approach allows one to map different enzymes of the pattern pathway into a single enzyme of a text network. It also efficiently handles cycles in patterns. The authors have applied their mapping tool in pairwise mapping of all pathways for four organisms (E. coli, S. cerevisiae, B. subtilis, and T. thermophilus species) and found a reasonably large set of statistically significant pathway similarities. Furthermore, they have compared the obtained set for when only tree pathways can be available as a pattern and that for when both nontree and tree pathways are available as a pattern. The chapter also shows that the authors' mapping tool can be used for identification of pathway holes and have proposed a framework for finding and filling these holes based on pathway mapping and database search.
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