OptStrain protocols

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OptStrain specifications

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Unique identifier OMICS_06453
Name OptStrain
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for OptStrain

OptStrain in pipeline

2012
PMCID: 3444828
PMID: 22997515
DOI: 10.1155/2012/323472

[…] database that allows for a specified level of biomass production in the resulting model. metaflux [] is an automated approach to find missing reactions, exchange reactions, and biomass metabolites. optstrain [] determines the maximum possible yield of a desired product based on the inclusion of all reactions in a universal database and then finds the minimum number of reactions […]


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OptStrain in publications

 (17)
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] the minimal number of genetic interventions). likewise, if the host organism is predefined, then it is also possible to minimize the number of heterologous reactions that need to be added (e.g., in optstrain and mre ). this is a plausible objective as dealing with heterologous enzymes in metabolic engineering project often poses a different set of challenges including that of enzyme activity, […]

PMCID: 5662904
PMID: 29123506
DOI: 10.3389/fmicb.2017.02060

[…] growth (). soon thereafter, a series of optknock-derived programs have been developed for various gene manipulations other than knock-out, such as optgene (), optforce (), optorf (), optreg (), and optstrain (). moma is a computational tool that calculates the changes to reaction fluxes when a gene is deleted. a result in an optimal flux state is seen with moma which is closest resembles […]

PMCID: 5221824
PMID: 28068354
DOI: 10.1371/journal.pone.0168725

[…] in mathematics and enable biotechnological analysis of pathways to increase the yield of important metabolites []. a number of the stoichiometric methods, such as cfp [–], pathtracer [], optstrain [], optstoic [], ncga [], and retropath [], has been proposed., graph-based pathfinding methods find possible metabolic pathways converting a given start compound to a given target compound […]

PMCID: 5035732
PMID: 27725824
DOI: 10.3389/fpls.2016.01421

[…] for sets of gene knockouts that lead to the production of desired products () and can be used for the same purpose which can resist the plant from harmful microbial compounds. on the other hand, optstrain that not only allows gene knockouts, but also incorporate novel enzyme-coding genes from different species to a given microbial genome (). more recently, optreg was developed, searching […]

PMCID: 5516863
PMID: 28725470
DOI: 10.1038/npjsba.2016.9

[…] models (genome-scale or not) is finding the maximal theoretical yield of product and the distribution of fluxes in central metabolism that leads to the optimal yield. algorithms such as optstrain can search reaction databases and find additional reactions that could be added to the network to improve theoretical yield. second, stoichiometric models can be used to predict the effects […]


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OptStrain institution(s)
Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA

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