Planes Francisco J, Beasley John E
Mathematical Sciences, Brunel University, Uxbridge, UB8 3PH, UK.
Brief Bioinform. 2008 Sep;9(5):422-36. doi: 10.1093/bib/bbn018. Epub 2008 Apr 24.
Advances in the field of genomics have enabled computational analysis of metabolic pathways at the genome scale. Singular attention has been devoted in the literature to stoichiometric approaches, and path-finding approaches, to metabolic pathways. Stoichiometric approaches make use of reaction stoichiometry when trying to determine metabolic pathways. Stoichiometric approaches involve elementary flux modes and extreme pathways. In contrast, path-finding approaches propose an alternative view based on graph theory in which reaction stoichiometry is not considered. Path-finding approaches use shortest path and k-shortest path concepts. In this article we give a critical overview of the theory, applications and key research challenges of stoichiometric and path-finding approaches to metabolic pathways.
基因组学领域的进展使得在基因组规模上对代谢途径进行计算分析成为可能。文献中对代谢途径的化学计量学方法和路径寻找方法给予了特别关注。化学计量学方法在试图确定代谢途径时利用反应化学计量。化学计量学方法涉及基本通量模式和极端途径。相比之下，路径寻找方法基于图论提出了一种不同的观点，其中不考虑反应化学计量。路径寻找方法使用最短路径和k最短路径概念。在本文中，我们对代谢途径的化学计量学方法和路径寻找方法的理论、应用及关键研究挑战进行了批判性综述。
