During last decades, biotechnology advances allowed to gather a huge amount of biological data. This data ranges from genome composition to the chemical interactions occurring in the cell. Such huge amount of information requires the application of complex algorithms to reveal how they are organized in order to understand the underlying biology. The metabolism forms a class of very complex data and the graphs that represent it are composed of thousands of nodes and edges. In this thesis we propose an approach to modularize such networks to reveal their internal organization. We have analyzed red blood cells' networks corresponding to pathological states and the obtained in-silico results were corroborated by known in-vitro analysis. In the second part of the thesis we describe a learning method that analyzes thousands of sequences from the UniProt database to predict the N-alpha-terminal acetylation. This is done by automatically discovering discriminant motifs that are combined in a binary decision tree manner. Prediction performances on N-alpha-terminal acetylation are higher than the other published classifiers.