ABSTRACT
Due to some unknown reason,1 nature has organized the blue-print of a living organism along a line. Thus nucleotides on a strand of DNA or amino acids on a protein sequence (the primary structure) or genes on a chromosome are linearly arranged and the study of strings has been an important component in the general area of bioinformatics. But sometimes, there is a deviation from this clean organizational simplicity,
for instance, a cell’s metabolic network, as we understand it. A metabolic pathway is a series of chemical reactions that occur within a cell, usually catalyzed by enzymes, resulting in the synthesis of a metabolic product that is stored in the cell. Sometimes, instead of creating such a product, the pathway may simply initiate another series of reactions (yet another pathway). Various such metabolic pathways within a cell have a large number of common components and thus form the cell’s metabolic network. Figure 12.1 shows an example. To study and gain an understanding in a domain such as this, one abstracts
the organization of this information as a graph. A graph captures this kind of complex interrelationships of the entities. Continuing the theme of this book, we seek the recurring structures in this data.
