knockout

[haniye jafari]

Hi

I need an algorithm that delete all reactions ( like =>simple Opt Knock.m) ,and find those reaction deletions that decrease biomass, then use these deletions to increase production yield. does anybody know this algorithm?  please sent me the mfile

[Will]

Hi,

I would be careful with the approach of individual reaction knockouts.  Since the mapping of genes > proteins > reactions is many-to-many, it may not be possible to implement (in the lab) the knockout of specific reactions, only of specific genes.

I would also say that just because a knockout impedes biomass accumulation, this does not necessarily imply improved production of a (secondary?) metabolite.  Even if yield is increased, it might produce sickly cells, thus impeding total target metabolite production.  Someone with a more biotech background might be able to help you with this.

That said, if you do still wish to analyse each reaction knockout in turn, just set the upper and lower bounds of each reaction in turn to 0, which will 'turn off' the reaction.  Then you can optimise for biomass growth.  Remember to reset the bounds for each reaction to their initial values before testing the next reaction!

Cheers,

Will.

[Thomas Pfau]

Hi,

To find reactions that decrease flux through a target, simply use singleRxnDeletion.m

Afterwards you can check whether any reaction with a grRatio < 1, whether it increases your by-product yield.

However I would agree with Will, that this might be difficult to reproduce in the lab and singleGeneDeletion is probably more appropriate.

Best

Thomas

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[haniye jafari]

Hi . Tnx to you ,for your help , i just want to use this for in silico model in my project , i dont want to test in lab. 

Tnx again☺

On 6 Sep 2017 13:55, "Thomas Pfau" <thoma...@uni.lu> wrote:

Hi,

To find reactions that decrease flux through a target, simply use singleRxnDeletion.m

Afterwards you can check whether any reaction with a grRatio < 1, whether it increases your by-product yield.

However I would agree with Will, that this might be difficult to reproduce in the lab and singleGeneDeletion is probably more appropriate.

Best

Thomas

On 2017-08-31 11:14, Will wrote:

Hi,

I would be careful with the approach of individual reaction knockouts.  Since the mapping of genes > proteins > reactions is many-to-many, it may not be possible to implement (in the lab) the knockout of specific reactions, only of specific genes.

I would also say that just because a knockout impedes biomass accumulation, this does not necessarily imply improved production of a (secondary?) metabolite.  Even if yield is increased, it might produce sickly cells, thus impeding total target metabolite production.  Someone with a more biotech background might be able to help you with this.

That said, if you do still wish to analyse each reaction knockout in turn, just set the upper and lower bounds of each reaction in turn to 0, which will 'turn off' the reaction.  Then you can optimise for biomass growth.  Remember to reset the bounds for each reaction to their initial values before testing the next reaction!

Cheers,

Will.

On Wednesday, August 30, 2017 at 10:02:38 PM UTC+1, haniye jafari wrote:

Hi

I need an algorithm that delete all reactions ( like =>simple Opt Knock.m) ,and find those reaction deletions that decrease biomass, then use these deletions to increase production yield. does anybody know this algorithm?  please sent me the mfile

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L-4367 Belvaux
Tel: (+352) 46 66 44 5309
Email: thoma...@uni.lu

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