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Moderna mRNA sequence released to GitHub [pdf]

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Re: Moderna mRNA sequence released to GitHub [pdf]

#281
post #274
post #263

The Human Genome Project was completed almost two decades ago, and somebody solved the protein folding problem recently. Why are we still doing genetics at the machine code level? Shouldn't we have some compilers, assemblers and linkers by now?

My thought exactly. So this thing is like a VM with a bunch of primitive opcode, why can’t someone write a higher-level language or at least some gadgets

The problem with trying to program genetics is that there is a bunch of code already running on the system and every variable is a global. You can't just start up a new program with minimal impact on the stuff that is already running, like you can in most human-made computers. Also don't forget that the extremely simplified version of the running system looks like this: https://www.sigmaaldrich.com/technical-documents/articles/bi...

Re: Moderna mRNA sequence released to GitHub [pdf]

#282
post #51

If my little knowledge from biology class serves me correct, RNA uses Udenine instead of Thymine. But in this document it uses T. Can somebody explain to me why?

Note that independently of the notation used the mRNA of those vaccines use even more "weird" bases, such as 1-methyl-3’-pseudouridylyl, to make the vaccine mRNA not be detected by the immune system [1].

[1] https://berthub.eu/articles/posts/reverse-engineering-source...

Re: Moderna mRNA sequence released to GitHub [pdf]

#283
post #272

I compared the spike encoding regions, and it looks like they're quite different...I wonder if the codons wind up coding for different amino acids. And who got it right?

Their codon compositions were optimized differently, but both coding regions translate to the same amino acid sequence.

Re: Moderna mRNA sequence released to GitHub [pdf]

#284
post #70
post #31

I'm sure it's more complex than I grasp as a layperson, but I'm utterly amazed at how simple this _appears_. I get the feeling that this is something I have a better chance of understanding than the average SaaS Terms and Conditions. I expected to have to scroll through pages upon pages of indecipherable text. Instead it's no bigger than a large paragraph of text, and I can easily fit it on my screen.

The protein they're trying to manufacture is indeed quite simple - AFAIU both BioNTech and Moderna put together their sequences in a weekend. (Though there was a more involved process of winnowing down the sequences for the most effective ones.) The technically challenging parts are: - delivery mechanism: you need to take a very unstable molecule, protect it from the environment - both external, and when inside the p…

Would it be possible to use the same delivery mechanism for other mRNA sequences?

Re: Moderna mRNA sequence released to GitHub [pdf]

#285

Earlier quoted context omitted.

It really is that “simple.” Getting it designed and building it is more difficult. At its core, it’s a piece of mRNA that creates a protein. That code gets transcribed into a protein (often those are relatively short). That protein then triggers your bodies immune response, which trains it to attack covid19. Inject this mRNA into a cell and it’ll create the protein. Anything can be injected at this point once the mec…

Which makes me wonder. Could you place the entire virus genome in these liposomes and get them to hijack the machinery to make an entire virus? Like plasmid but for viral structures?

Why would you want to do that if you can use the virus itself as the delivery mechanism?

Re: Moderna mRNA sequence released to GitHub [pdf]

#286

Rather disappointingly, neither sequence includes the string 'GATTACA'

A given combination of 7 bases has a probability of occurring of 1/16,384. Since the COVID genome is about 22k bases long I guess you have pretty good chance of it appearing in there somewhere. This assumes uniformity, which of course is not true. COVID’s genome is under crazy intense selection pressure!

The sequence GATTCA appears 4 times in the reference version of the COVID genome :) (Go to https://www.ncbi.nlm.nih.gov/nuccore/NC_045512, pick "Find in this Sequence" on the right)

Re: Moderna mRNA sequence released to GitHub [pdf]

#287
post #89

Earlier quoted context omitted.

InstallGene by Flexera

Just waiting for first copy protection mechanism for mRNA. SafeGene and SecuGene here we come :o

Can you imagine, the greedy folk would want some sort of Widevine in humans.

Re: Moderna mRNA sequence released to GitHub [pdf]

#288
post #263

The Human Genome Project was completed almost two decades ago, and somebody solved the protein folding problem recently. Why are we still doing genetics at the machine code level? Shouldn't we have some compilers, assemblers and linkers by now?

If I remember correctly "solving" protein folding was essentially some high probability prediction that state A transform to state B with some reasonably high chance, on a big dataset. Or something like that anyway. It's as far from high level work with genetics as creating nanotubes a few molecules long in lab manually is away from industrial production.

Re: Moderna mRNA sequence released to GitHub [pdf]

#289
post #70
post #31

I'm sure it's more complex than I grasp as a layperson, but I'm utterly amazed at how simple this _appears_. I get the feeling that this is something I have a better chance of understanding than the average SaaS Terms and Conditions. I expected to have to scroll through pages upon pages of indecipherable text. Instead it's no bigger than a large paragraph of text, and I can easily fit it on my screen.

The protein they're trying to manufacture is indeed quite simple - AFAIU both BioNTech and Moderna put together their sequences in a weekend. (Though there was a more involved process of winnowing down the sequences for the most effective ones.) The technically challenging parts are: - delivery mechanism: you need to take a very unstable molecule, protect it from the environment - both external, and when inside the p…

Additional reading (was posted here some time ago):

https://blogs.sciencemag.org/pipeline/archives/2021/02/02/my...

Why manufacturing of these vaccines is a hard part.

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