81–90 of 133 posts
To read the data out are they basically doing de novo assembly on the sequenced reads? How are they handling all of the errors in gene sequencing? How about assembly errors? Long repeats?
Earlier quoted context omitted.
If your strand length is less than or equal to the read length of your sequencer, and you have the address blocks at the start of every sequence, you don't really need to worry about assembly. Read depth and/or a checksum of some kind will take care of errors in sequencing, and with short strands or compression of some kind, long repeats aren't much of a problem either.
Thanks, that makes sense. But how to you get the address block at the start of each sequence?
If you store data onto 50 DNA strands, can you always read back all the data from all 50 strands, or does one need to store multiple copies of each in case the sequencer can't "find" a particular strand? If one does need multiple copies, it would seem that this method suffers from the coupon collector's problem [1] (i.e. to collect all 50 strands requires collecting 225 random strands on average), and that the retrie…
To sequence we used about ~100x synthetic coverage on average and ~1000x sequencing coverage; so that's a whole lot of coverage. even then we did have 10 bit errors, but all the data blocks were recovered
Wow. For scale, the Internet Archive had 5.8 petabytes of data in December 2010 [1] - so, about 9 grams' worth. How much did this cost? [1] http://archive.org/web/petabox.php
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Flash drives also have all of the necessary equipment for it to be read. I wonder how much data per gram the actual storage part of the flash drive actually is. I doubt it's better than DNA, but I think it might be disingenuous for the article to be offering the analogy to hard drives without taking into account the extra read/write hardware.
agreed, it should be comparied to other arhival media like tape drives; but it's still pretty similar; we compare in our paper a hard drive platter rather than a drive itself. even then we are approximately ~million fold more dense
Earlier quoted context omitted.
To sequence we used about ~100x synthetic coverage on average and ~1000x sequencing coverage; so that's a whole lot of coverage. even then we did have 10 bit errors, but all the data blocks were recovered
I'm sorry, can you clarify what that means? You wrote each piece of data 100 times? what does the 1000 refer to?
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.
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.
Earlier quoted context omitted.
To sequence we used about ~100x synthetic coverage on average and ~1000x sequencing coverage; so that's a whole lot of coverage. even then we did have 10 bit errors, but all the data blocks were recovered
I'm sorry, can you clarify what that means? You wrote each piece of data 100 times? what does the 1000 refer to?
Why binary if DNA naturally has 4 bits?
I imagine this could be solved by ensuring that every helix starts out with something like a byte order mark that would distinguish the two strands reliably.
Storage density could be further increased by a constant factor if more kinds of bases were used, or if they could use single-strand DNA/RNA instead (which would probably require some chemical means of ensuring that a free strand doesn't accidentally bind to something else).
I really liked their paper. Its a bit less over the top than the extremetech guys but hey, that is the difference between pop journalism and science. Clearly with some form of fountain code or LDPC codes you will be able to get the data back, but what struck me is that I always thought of DNA as relatively unstable, in the sense that cells decay/die etc, but the fact that just sitting there, DNA which isn't expressin…
do you have a link to their paper?