METATOOL:: for studying metabolic networks
METATOOL:: for studying metabolic networks
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DOI：
10.1093/bioinformatics/15.3.251
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发表时间：
1999-03-01
期刊：
影响因子：
5.8
通讯作者：
Schuster, S
中科院分区：
文献类型：
--
作者：
Pfeiffer, T;Sánchez-Valdenebro, I;Schuster, S
动机：为了从生物化学和/或基因组序列数据重建代谢途径，必须测试途径的化学计量和热力学可行性。这是通过表征稳态下通量分布的容许区域来实现的。这个区域被称为凸基的东西所覆盖。“基本通量模式”的概念提供了一种数学工具来定义在给定代谢网络中可行的所有代谢途径。此外，我们将“酶亚群”定义为在系统的所有稳定状态下以固定流量比例一起操作的酶组。本文简要回顾了以前提出的计算凸基和基本模式的算法，提出了一种新的算法，用于检测给定网络中的所有酶子集。其特征在此概述。该算法说明了从糖代谢的一个例子。
Motivation: To reconstruct metabolic pathways from biochemical and/or genome sequence data, the stoichiometric and thermodynamic feasibility of the pathways has to be tested. This is achieved by characterizing the admissible region of flux distributions in steady state. This region is spanned by what can be called a convex basis. The concept of 'elementary flux modes' provides a mathematical tool to define all metabolic routes that are feasible in a given metabolic network. In addition, we define 'enzyme subsets' to be groups of enzymes that operate together in fixed flux proportions in all steady states of the system.Results: Algorithms for computing the convex basis and elementary modes developed earlier are briefly reviewed A newly developed algorithm for detecting all enzyme subsets in a given network is presented All of these algorithms have been implemented in a novel computer program named METATOOL, whose features are outlined here. The algorithms are illustrated by an example taken from sugar metabolism.