<p>To generate flux balance, one should now the stoichiometric numbers of all the reactions that are taking place, as well as the conditions (that could affect the reactions). I am not sure we have enough knowledge, time and computationally power to do this.</p>

<p>At the moment I'm only aware of a <a href="https://www.cell.com/abstract/S0092-8674%2812%2900776-3" rel="nofollow noreferrer">paper</a> simulating the <em>Mycoplasma genitalium</em> cell. But I'm not sure it was worth the effort as I haven't seen replicated or redone with other species, perhaps the model was not accurate enough to be worth it. </p>

<p>The tools used are <a href="http://www.wholecell.org/" rel="nofollow noreferrer">here</a>. The licenses are not a standard, but at least they seem free.</p>

CC BY-SA 4.0
2018-06-18T23:09:35.593Z
Thanks. What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database.
LifeWorks
CC BY-SA 4.0
2018-06-19T07:12:09.400Z
Which would be your input? A list of genes? This is trivial to do, but you don't know how many active sites are in an enzyme nor if there is any inhibitor, and you would need to know the initial concentrations to see if you reach a steady state or not, and what is your end point is also a variable you should define
llrs
CC BY-SA 4.0
2018-06-04T07:31:49.393Z
2018-06-04T10:06:25.940Z
2018-06-04T10:06:25.940Z
llrs
<p>Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a <a href="https://en.wikipedia.org/wiki/Flux_balance_analysis" rel="nofollow noreferrer">flux balance analysis</a> model out of them?</p>

<p>What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database.</p>

<sequence-analysis><sequence-annotation><modelling>
Is there any tools that can generating FBA model from genome sequences or proteome sequences?
# Is there any tools that can generating FBA model from genome sequences or proteome sequences?

(Asked by: username_0 on 2018-06-04)

Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a [flux balance analysis](https://en.wikipedia.org/wiki/Flux_balance_analysis) model out of them?

What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database.

**Tags:** sequence-analysis, sequence-annotation, modelling

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## 1 answers

### Answer by username_1 on 2018-06-04. Score: 2

To generate flux balance, one should now the stoichiometric numbers of all the reactions that are taking place, as well as the conditions (that could affect the reactions). I am not sure we have enough knowledge, time and computationally power to do this.

At the moment I'm only aware of a [paper](https://www.cell.com/abstract/S0092-8674%2812%2900776-3) simulating the *Mycoplasma genitalium* cell. But I'm not sure it was worth the effort as I haven't seen replicated or redone with other species, perhaps the model was not accurate enough to be worth it.

The tools used are [here](http://www.wholecell.org/). The licenses are not a standard, but at least they seem free.

> **Comments:**
> **username_0**: Thanks. What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database.  
> **username_1**: Which would be your input? A list of genes? This is trivial to do, but you don't know how many active sites are in an enzyme nor if there is any inhibitor, and you would need to know the initial concentrations to see if you reach a steady state or not, and what is your end point is also a variable you should define  

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