sAnalyzer

A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of pathways. This tool can be used for the metabolic pathway supergraph construction using reactions taken from the KEGG database.

 

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A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of pathways. This tool can be used for the metabolic pathway supergraph construction using reactions taken from the KEGG database.

SAnalyzer tool is a set of algorithms for metabolic pathways construction. SAnalyzer reads all necessary data from the KEGG database REST web service and processes it in real-time. Algorithms are realized in M scripts that can be placed on the local PC and launched from the Matlab command windows. The construction algorithm of possible metabolic pathways construction is independent software that can return nodes and edges of the constructed graph. The tree construction proceeds recursively, beginning from the starting metabolite, i.e. initial substrate of the pathway of interest given by industrialists, as a root of a tree. We can call it a “super graph” which contains all possible pathways from the input substrate for fixed levels count. Construction is performed based on the graph theory methods.

 

The sAnalyzer is developed in MATLAB.

 
 

 

Citation

Meitalovs J., Stalidzans E. (2015) Impact of Thermodynamic Constraint to the Solution Space of Metabolic Pathway Design Using sAnalyzer Tool. Baltic Journal of Modern Computing, 3(3), pp.164–178. View full text.

Meitalovs, J., Stalidzans, E. (2013) Connectivity analysis of metabolites in synthetic metabolic pathways. In Proceedings of the 12th International Scientific Conference “Engineering for Rural Development, May 23–25, 2013, Jelgava, Latvia, pp. 435–440. View full text.