Efficient Alignments of Metabolic Networks with Bounded Treewidth

The authors in this chapter develop a computationally much more efficient approach based on homomorphisms and homeomorphisms, allowing toleration of the divergence within the alignment of metabolic pathways. Although metabolic pathways may exhibit fairly complex structures, their analysis of existing databases shows that corresponding graphs have very restricted treewidth for which very efficient alignment algorithms can be developed. They present the first polynomial time algorithm for optimal alignment of metabolic pathways with bounded treewidth. In the chapter, authors give a brief overview of current state-of-the-art methods in metabolic pathway/network alignment and how they can be used in automatic data curating. The generalized network alignment problem is formulated and tree decomposition-based solution is described here. Finally, the chapter describes application of the network alignment algorithm to finding and filling holes in metabolic networks.