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Comment by conanite | Hacker News Reader

They're using T and G for a 1, and A and C for a 0; why not double the density and get two bits from each letter?

  T = 00
  G = 01
  A = 10
  C = 11

for example.

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we didn't because we wanted to avoid particular sequence features that are difficult to synthesize and sequence. we probably could have gotten away with something like 1.8 bits per base, but we were already doing fine on density, so we thought a 2x hit wouldn't be that bad.

i should clarify, because of extra sequence and the address barcode, we are technically only 0.6 bits/base

Base pairs. They don't occur individually.

IANA DNA expert, but they still seem to be ordered [1]. So a possible scheme to increase data density could be:

AT = 00

TA = 01

CG = 10

GC = 11

The trick would be to always correctly identify which is the left and which is the right strand. I don't know if that is possible in practice though.

[1] http://en.wikipedia.org/wiki/Base_pair#Examples

Ribosomes seem to manage just fine. :)

You just encode a big marker (making sure it's not a palindrome-paired version of itself!) as a header. If you see that, it's a correct order. If not, it's not.

This header idea is great because then you only need to keep one strand and can toss the other, potentially quadrupling the amount of data storage (I'm assuming you can keep single strands of DNA stable).

[Left strand]

A = 00

T = 01

C = 10

G = 11

[Right strand]

T = 00

A = 01

G = 10

C = 11

Anyone know these guys at Harvard, b/c this might be a way to put, at most, 2800 terabytes in a gram? (I don't know how long the header sequences would have to be).

It's possible to have single stranded DNA, but you'd have problems with error correction.

Let's say DNA breaks, or some errors appear in the code. Thanks to the double stranded structure it's "quite easy" to repair the code.

Besides that, it's not the density which is a problem right now, but the access speed. The amount of data in DNA is so immense that doubling the density won't give any practical improvements for decades to come - if ever.

Having said that, if I'm not mistaken, some viruses are encoded by single stranded DNA & ssRNA. I'm not sure, but the density might be the reason for that.

I don't think you can simply toss one of the strands. DNA is so compact because of the way it coils, and you likely lose that if you only have one strand.

I suspect that George's lab used a sensible encoding scheme. They're fairly sharp.

I can't find a copy of the original article, but it's certainly more informative than some science journalism fluff piece.

They might not have used a "coding" scheme at all, if they were interested in characterizing the frequency and types of errors.

that's irrelevant since you have 2 strands that are mirror copies of each other. just prefix your data with a single A, if it's read as a T, just invert the bits of the rest of the strand.

I'm not sure exactly why they decided on that encoding, I suspect there is some technical reason such as error tolerance.

it's to avoid sequence features which are problematic like high GC content

Ah, interesting. In natural DNA this is achieved by using a more complex encoding scheme (3 base pairs -> one amino acid), combined with the vast majority of DNA not encoding genes directly.

well, the genetic code has presumably evolved to evolve; it's unclear that it's evolved to preserve information

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