%0 Journal Article
%T Inferring branching pathways in genome-scale metabolic networks
%A Esa Pitk£¿nen
%A Paula Jouhten
%A Juho Rousu
%J BMC Systems Biology
%D 2009
%I BioMed Central
%R 10.1186/1752-0509-3-103
%X In this paper, we introduce a computational method, ReTrace, for finding biochemically relevant, branching metabolic pathways in an atom-level representation of metabolic networks. The method finds compact pathways which transfer a high fraction of atoms from source to target metabolites by considering combinations of linear shortest paths. In contrast to current steady-state pathway analysis methods, our method scales up well and is able to operate on genome-scale models. Further, we show that the pathways produced are biochemically meaningful by an example involving the biosynthesis of inosine 5'-monophosphate (IMP). In particular, the method is able to avoid typical problems associated with graph-theoretic approaches such as the need to define side metabolites or pathways not carrying any net carbon flux appearing in results. Finally, we discuss an application involving reconstruction of amino acid pathways of a recently sequenced organism demonstrating how measurement data can be easily incorporated into ReTrace analysis. ReTrace is licensed under GPL and is freely available for academic use at http://www.cs.helsinki.fi/group/sysfys/software/retrace/ webcite.ReTrace is a useful method in metabolic path finding tasks, combining some of the best aspects in constraint-based and graph-theoretic methods. It finds use in a multitude of tasks ranging from metabolic engineering to metabolic reconstruction of recently sequenced organisms.Genome-scale metabolic reconstructions from a variety of organisms have become available in recent years [1]. At the same time, data from different organism-specific networks has been collected into "universal" metabolic databases such as KEGG [2] and BioCyc [3]. This has enabled comparative analyses of metabolism over multiple organisms [4,5], and proven useful in drug discovery [6], metabolic flux analysis [7] and metabolic engineering [8] tasks.A typical way to query a metabolic model is to ask whether a biologically realistic connect
%U http://www.biomedcentral.com/1752-0509/3/103