Abstract: A system and method for estimation of functional potential of pathways in genomes/meta-genomes is provided. Initially seed modules are identified and a multi-dimensional tag map is created. Further, pathway annotation is done using a novel 6Q annotation step. Hidden Markov Model (HMM) based search augmented with an analysis of gene context is used to refine the modules using a graph theory based approach. The method uses the multidimensional module tag map to build a backend knowledge base and use the same for an iterative literature search to verify the clustered organization of genes within a pathway. Finally, a score is assigned to compute the contribution of each pathway within the genome/meta-genome.