FindPath: a Matlab solution for in silico design of synthetic metabolic pathways

被引：13

作者：

Vieira, Gilles ^{[1
,2
,3
]}

Carnicer, Marc ^{[1
,2
,3
]}

Portais, Jean-Charles ^{[1
,2
,3
]}

Heux, Stephanie ^{[1
,2
,3
]}

机构：

[1] Univ Toulouse, INSA, UPS, INP,LISBP, F-31077 Toulouse, France

[2] INRA, UMR792, F-31400 Toulouse, France

[3] CNRS, UMR5504, F-31400 Toulouse, France

来源：

BIOINFORMATICS | 2014年 / 30卷 / 20期

关键词：

PREDICTION; CEREVISIAE; MODELS;

D O I：

10.1093/bioinformatics/btu422

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A Summary: Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files.

引用

页码：2986 / 2988

页数：3

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