Research Of Metabolic Pathway Alignment Method Based On Enzyme Graph

With the accumulation of high-throughput genomics,proteomics and metabolism data,tens and thousands of experimental data make it possible for modeling metabolic pathway which is extremely large and complex,and models of metabolic pathways become more and more accurate.Metabolic pathways show how different molecules interact with each other to perform vital functions.Metabolic pathways,an important class of biological networks,represent how different compounds are transformed through various reactions.Analyzing these pathways is essential in understanding the machinery of living organisms.From the topological structure and biological properties of metabolic pathways,this paper has done some research which aimed at the complex metabolic pathways,and the main work is as follow:(1)For existing metabolic pathway reconstruction method is easy to generate redundant data,and can't distinguish whether the interaction between the enzymes is bilateral,this paper has put forward a new method for reconstruction of metabolic pathways based on PATHWAY database,and finished the reconstruction of enzyme graph and substrate graph.The method downloads relative XML document from the database which records enzyme data and species-specific metabolic pathway data and analyzes the internal contact,after that we extract the key information we need and add them to the local database,then through the matching of correlation fields we express the metabolic pathways as enzyme graph and substrate graph,so that we can achieve the goal of reconstruct the metabolic pathways.The experimental results show that,the enzyme graph and substrate graph by reconstruction can be more accurately to represent the direction of metabolic pathways and when comparing with the original graph from PAHTWAY database we find that there is no redundant data and missing data.(2)The alignment of metabolic pathways belongs to alignments of complex networks.Most of the existing methods limited the topology of metabolic pathways to finish the alignment.In order to overcome this shortcoming,this paper has proposed a method based on topological similarity and enzyme similarity to conduct global alignment of metabolic pathways.By inputting the overall metabolic pathway,this method first calculates topological similarity and enzyme similarity of the node and weights them to obtain the similarity score matrix of nodes.Then by combining with the interaction score matrix we get the similarity score matrix.Finally by using greedy search we extract the best results and interaction score will be iterative update during the search process,thereby it will increase the likelihood of match of the similar nodes.Experimental results show that,the method based on topological similarity and enzyme similarity can recognize the conserved modules within species or between species,and match the same or similar enzymes,so that we can identify missing or ambiguous enzymes.At the same time,global alignment which is not need to restrict the topology can be as much as possible preserve biological integrity and find more conservative module so that reflects the biological significance of alignment.