Custom Nucleotide Sequence Codons?

[gf11221]

Hello there guys, i'm new on this forum so nice to meet you all!

By the way, i am thinking about writing your own nucleotide sequence codons for a DNA/RNA/Gene/Genome/Chromosome for my Synthetic Life Simulation which allows the user to evolve from a simple cell to a complete organism via user's natural selection by eating other organisms...

But i want to know where can i get some complete DNA/RNA/Gene/Genome/Chromosome codons?

For example, here is my own DNA/RNA/Gene/Genome/Chromesome codon for a Nascent's Cell(I 'm making my own virtual cell that can evolve via written codons on a txt document)


:TYPE:CELL
:EVO_LVL:0
:CODON_START:

GAT
AAAT
CT
GGTCTT
ATT
TCC

:CODON_END:


Well, the code above is still on the work but i need to collect some codons of an existing cell like M.MYCOIDES Cell nucleic acid sequence

[mishrashubham]

Well I don't think programs use the actual DNA sequence to run their simulations; instead they use many parameters such as effective population size, rate of recombination and mutation, and migration parameters. But then I am not much into simulation programs (as of yet) so I might be wrong.

I would like to ask, if you don't mind; how are you going to implement the DNA code in your program? Since real life genes work by making proteins which in turn make the organism, I can't see how the DNA sequence could be used as input for a simulation.

Here are some resources if you need the sequences.
http://www.ncbi.nlm.nih.gov/nuccore
http://www.ncbi.nlm.nih.gov/sites/genome

[Ryan_m_b]

Welcome to PF. Like mishrashubham I'm a bit unclear about how you are trying to make this simulation work? Genes create proteins which utilise resources from the environment to create countless metabolic pathways (http://en.wikipedia.org/wiki/Metabolic_pathway), the emergent property of these pathways is an organism.

DNA alone will not work, sure you might be able to code it so that if X gene is present the simulated organism has X1 capability but you need to know the proteome (http://en.wikipedia.org/wiki/Proteome), transcriptome (http://en.wikipedia.org/wiki/Transcriptome) and epigenome (http://en.wikipedia.org/wiki/Epigenetics) so that you can ultimately work out the phenome (http://en.wikipedia.org/wiki/Phenome). This isn't possible at the moment as we lack knowledge of these things for most species and I don't think the sum computing power on Earth could handle all the variables for simulating even a single celled organism at a molecular level.

If your DNA is just a seed code that doesn't relate to real life in any way (other than using the same letters, GATC, in the code) why do you want existing sequences?

[mishrashubham]

This isn't possible at the moment as we lack knowledge of these things for most species and I don't think the sum computing power on Earth could handle all the variables for simulating even a single celled organism at a molecular level.

Exactly!

[gf11221]

I would like to ask, if you don't mind; how are you going to implement the DNA code in your program? Since real life genes work by making proteins which in turn make the organism, I can't see how the DNA sequence could be used as input for a simulation.


That's easy to say but hard to do, i have a friend of mine who lives in canada and he is a microbiologist who help me to do this simulation w/ some help from their professors.

If i were right, this is the basic sequence of a single DNA Chain for a cell/organism to move around:

:NAME:NASCANT_CELL_01
:TYPE:CELL
:EVO_LVL:1
:CODON_START:
:CHAIN_1_START:
A===T
G===C
T===A
C===G
G===C
A===T
:CHAIN_2_STOP:
:CODON_END:

For a while, the simulation program we're working on wasn't yet able to control more than 1 virtual cell or organism per generated space.

Also this program might have a DDA System which allows a person to control the selected organism and eat other organism and evolve through natural selection

@ryan_m_b
The core engine of the simulation program can identify what kind or which part of a DNA/RNA should response according to the input and the keywords i'm using like :CODON_START: and :CODON_END:

And yes, its possible to make a simulation of an existing life but will requires the complete DNA/RNA Chains including the genes and other meterials needed to make a cell/organism work

[Ryan_m_b]

The core engine of the simulation program can identify what kind or which part of a DNA/RNA should response according to the input and the keywords i'm using like :CODON_START: and :CODON_END:

And yes, its possible to make a simulation of an existing life but will requires the complete DNA/RNA Chains including the genes and other meterials needed to make a cell/organism work

I don't think this is really possible. Genes don't give well defined characteristics, they create proteins. You can't pick a gene and say "if my organism possesses this gene it has ability X".

[mishrashubham]

Also this program might have a DDA System which allows a person to control the selected organism and eat other organism and evolve through natural selection

What does DDA stand for?


And yes, its possible to make a simulation of an existing life but will requires the complete DNA/RNA Chains including the genes and other meterials needed to make a cell/organism work

That's exactly what we want to know. How will you use the actual DNA sequence in your program?

[gf11221]

I will need to type the sequences in a raw txt document just like what i did in the example of A,T,G, and C single chain mixture for a simple movements of a cell...

This thesis provides a unique game design methodology to realize player-centric Dynamic
Difficulty Adjustment (DDA) in video games, which creates optimized video game
experiences for different types of players.
Rather than offering player a passive DDA experience by analyzing incomplete in-game
data, this thesis uses Mihaly Csikszentmihalyi’s Flow theory and provides players with
subconscious choices to help them actively customize their optimal video game
experiences. It treats active DDA as a new parameter for analyzing video games and
seeks to address why certain video games had a wider appeal than others

I will use DDA for the simulation so the users can control each organism in flow

[Ryan_m_b]

I still don't understand how real life DNA sequences relate to what you are doing. As far as I can tell;


You are making an alife program
The code that determines cell characteristics will be written with CAGT as the letters
You want to make that code similar to real life.


The last bit is still confusing me.

[gf11221]

you said the answers you're looking for mate ;)

[Ryan_m_b]

Right ok, well the top two you can do but the last one; making the code similar to real life is going to be very hard - impossible depending on how you want to do it.

You could make it simple e.g. organisms with X gene produce X antibody that harms organisms within a certain radius but organisms with Y gene are immune (using the real DNA sequence for the antibody and the resistance). But this will not relate to real life. Genes can be mutated in a number of ways (http://en.wikipedia.org/wiki/Mutation#Classification_of_mutation_types). These different type of mutations often change the protein being expressed and this change can cause the protein to interact with the environment and various metabolic pathways in different ways. There is no way you are going to be able to simulate how this will work.

Genes create proteins, proteins work together with chemicals from the environment to form metabolic pathways. Working out the relationship between genome and phenome is not something that science has yet accomplished in any organism. I think your project is far to ambitious for what you are going to want to achieve.

[gf11221]

Yeah, by the way! I didn't made the program, i'm just he financial advisor and researcher for that project ;) Thanks for replying

[Ryan_m_b]

Perhaps you should pass on our questions to the programmer then. Unfortunately science is nowhere near capable of performing the tasks that you have set yourself.