title: TNA4OptFlux--a software tool for the analysis of strain optimization strategies.
abstract: 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.
  
  
  RESULTS
  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, together with extensive documentation.
authors: Department of Informatics/CCTC, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal.
authors: José P
authors: JP
authors: Pinto
authors: Rui
authors: R
authors: Pereira
authors: João
authors: J
authors: Cardoso
authors: Isabel
authors: I
authors: Rocha
authors: Miguel
authors: M
authors: Rocha
mesh_terms: D000465:Algorithms; D008660:Metabolism; D012984:Software
references: Bioinformatics. 2011 Feb 1;27(3):431-2
references: 21149340
references: Nature. 1998 Jun 4;393(6684):440-2
references: 9623998
references: Comput Methods Programs Biomed. 2010 May;98(2):191-203
references: 20047774
references: Nat Rev Genet. 2004 Feb;5(2):101-13
references: 14735121
references: Mol Syst Biol. 2007;3:121
references: 17593909
references: Mol Syst Biol. 2010 Jul;6:390
references: 20664636
references: BMC Syst Biol. 2010 Apr 19;4:45
references: 20403172
references: Nat Biotechnol. 2000 Mar;18(3):326-32
references: 10700151
references: BMC Bioinformatics. 2008 Nov 27;9:499
references: 19038030
references: IET Syst Biol. 2007 Mar;1(2):89-119
references: 17441552
references: Bioinformatics. 2009 Dec 15;25(24):3282-8
references: 19808881
references: Brief Bioinform. 2007 Jul;8(4):210-9
references: 17626066
references: Ernst Schering Res Found Workshop. 2002;(38):245-74
references: 12061005
references: Brief Bioinform. 2006 Jun;7(2):140-50
references: 16772264