FindPath：用于计算机合成代谢途径设计的 Matlab 解决方案。

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

机构信息

Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France and CNRS, UMR5504, F-31400 Toulouse, France.

出版信息

Bioinformatics. 2014 Oct 15;30(20):2986-8. doi: 10.1093/bioinformatics/btu422. Epub 2014 Jul 3.

DOI:10.1093/bioinformatics/btu422

PMID:24994891

Abstract

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.

AVAILABILITY AND IMPLEMENTATION

http://metasys.insa-toulouse.fr/software/findpath/.

CONTACT

heux@insa-toulouse.fr

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

已经开发出多种方法和计算工具来设计新的代谢途径。主要挑战是评估设计的途径在宿主生物中的代谢效率。本文介绍了 FindPath，这是一个统一的系统，用于根据细胞系统中的代谢效率对可能的途径进行预测和排序。该工具使用化学反应数据库生成可能的代谢途径，并利用基于约束的模型 (CBM) 来识别在给定宿主微生物中实现所需代谢功能的最有效合成途径。FindPath 可与 CBM 操作的常用工具一起使用，并使用标准的 SBML 格式作为输入和输出文件。