Transform Data into DNA picture

Question

[anasjamshed]

I have data in a text file format like this:

I want to make a DNA double helix figure on the basis of this data. How can I draw?

[WouterDeCoster]

Can you explain why you want to do this? This doesn't make sense to me.

[anasjamshed]

I am a jeweller so I want to make DNA design bracelet that showing the mutation

[swbarnes2]

Honestly, I think you should ask the person who is requesting this what they want. You really need to have a much more specific question to get help here. "How do I turn some genotypes into jewelry" is not really the kind of question you can get a good answer to here.

[ATpoint]

At this point I am genuinely wondering whether this is sarcasm or not...cannot tell.

[WouterDeCoster]

Yeah that too doesn't make any sense.

[swbarnes2]

You want to draw a picture with double helices 162 thousand bases long?

[anasjamshed]

I think i need to take common nucleotide

Answer 1

[Asaf]

Easy peasy, you ask Dall-E to draw it!

Draw a DNA double helix with CCTGG sequence

[anasjamshed]

How sir? Can you please explain more?

[Asaf]

I was joking. Dall-E is an AI server that generates figure "on demand". It was developed by OpenAI - the same company that lounched chatGPT recently.

[anasjamshed]

so you mean its paid

[Asaf]

No, it's not paid you can access it here: https://labs.openai.com/ it's just not doing a good job at this particular task

[anasjamshed]

what does genotype mean in rsid? What does it indicate?

Answer 2

[barslmn]

You can use something like this https://dna.rosety.com/ to draw the double helix and annotate rs id's manually on an image editor.

Or this https://tex.stackexchange.com/questions/520699/drawing-simple-dna-helix and add your rs id's in tikz.

[anasjamshed]

How can I annotate with mutations?

[barslmn]

If this is a one of you can do so in an image processor like gimp. If you're going use this a lot I suggest you look into tikz or other drawing plotting tools. https://www.overleaf.com/read/drxwyrqzybjn

[anasjamshed]

We simply can use paint to annotate RSIDs. But my question is how? what does genotype mean in rsid? What does it indicate?

How can I transform genotype into DNA double helix?

[barslmn]

These rsids are identifiers for specific alleles. Genotypes here indicates the alleles observed at that locus. https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism

There is no specific tool I know of that does what you're asking for.

[anasjamshed]

yes, I know there is no such tool that exists. My question is what is the meaning of AC in genotype? Does it mean A changes to C(nonsynonymous mutation)?

[barslmn]

Human genomes have two copies, one from mom one from dad. Any genotype other than rs4970383 is homozygous meaning person got the same alleles from both of their parents. On the other hand rs4970383 is heterozygous meaning person got two distinct alleles from their parents.

This data doesn't say which parent gave the which allele meaning, whether the A or C is from mother or father. This data also doesn't denotes a change from one allele to another.

[swbarnes2]

This is not how rs ids are used at all.

Over time, the coordinate systems of genomes might shift slightly. Rs IDs are just so that we have a constant identifier that does not change, even if the numbering system does.

I'm sure there are many, many many people who are homozygous at rs4970383.

[anasjamshed]

so my understanding is AC means , A comes from father and C comes from mother

[barslmn]

This data doesn't say which parent gave the which allele, We can't say whether the A or C is from mother or father.

[barslmn]

Yes, they're constant identifiers to alternative alleles.

OP is a jeweler so my guess is that this is actually someones SNP data. Those genotype column doesn't show alternative alleles of the SNPs from some database since this rs4970383 in particular is multi allelic but I think some SNP array result.

[anasjamshed]

what does this C>A / C>G means? C is changing to A and C is changing to G?