I'm new to this field so I'm not sure if my question makes sense at all. I'd like to cluster SNPs based on their location but the problem is the 3d structure of DNA and the current location encoding which is : chromosome number and position on the chromosome, which makes defining a distance impossible. Is there any unique location encoding available for the whole unwrapped DNA? Thanks.
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written
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alireza.mdi •
1 answer
To start with, I don't think you should see this 3D structure as something static. It's likely dynamic and changing interactions depending on "cellular environment".
You could have a look at TAD databases/browsers, to get an idea of which DNA segments are within an interacting domain. But this is not really a physical distance, more a functional group.
If that's not what you are looking for I'm afraid I misunderstood your question.
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The term "unwrapped" usually refers to non-nucleosome-bound DNA, but that doesn't seem to be what you are referring to -- what are you referring to?