TNA4OptFlux – a software tool for the analysis of strain optimization strategies

BMC Research Notes

Miguel Rocha³  Isabel Rocha²  João Cardoso¹  Rui Pereira²  José P Pinto³ 

[1] SilicoLife, Lda., Avepark, Taipas, 4830, Portugal;IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal;Department of Informatics/CCTC, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal

关键词: OptFlux;    Open-source software;    Topological analysis;    Metabolic networks;    Strain optimization;   

Others  :  1142809
DOI  :  10.1186/1756-0500-6-175

 received in 2013-01-07, accepted in 2013-04-19,  发布年份 2013

【 摘 要 】

Background

Rational approaches for Metabolic Engineering (ME) deal with the identification of modifications that improve the microbes’ production capabilities of target compounds. One of the major challenges created by strain optimization algorithms used in these ME problems is the interpretation of the changes that lead to a given overproduction. Often, a single gene knockout induces changes in the fluxes of several reactions, as compared with the wild-type, and it is therefore difficult to evaluate the physiological differences of the in silico mutant. This is aggravated by the fact that genome-scale models per se are difficult to visualize, given the high number of reactions and metabolites involved.

Findings

We introduce a software tool, the Topological Network Analysis for OptFlux (TNA4OptFlux), a plug-in which adds to the open-source ME platform OptFlux the capability of creating and performing topological analysis over metabolic networks. One of the tool’s major advantages is the possibility of using these tools in the analysis and comparison of simulated phenotypes, namely those coming from the results of strain optimization algorithms. We illustrate the capabilities of the tool by using it to aid the interpretation of two E. coli strains designed in OptFlux for the overproduction of succinate and glycine.

Conclusions

Besides adding new functionalities to the OptFlux software tool regarding topological analysis, TNA4OptFlux methods greatly facilitate the interpretation of non-intuitive ME strategies by automating the comparison between perturbed and non-perturbed metabolic networks. The plug-in is available on the web site http://www.optflux.org webcite, together with extensive documentation.

【 授权许可】

   
2013 Pinto et al.; licensee BioMed Central Ltd.

【 图 表 】

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