9 ms·
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
by colanderman 14y ago
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 retrieval rate could be improved by using a fountain code [2], which allows each strand to simultaneously encode data at multiple addresses, which would decrease the number of strands required to be sampled to only slightly more than the number of strands worth of data requested.
[1] http://en.wikipedia.org/wiki/Coupon_collectors_problem http://en.wikipedia.org/wiki/Coupon_collectors_problem
[2] http://blog.notdot.net/2012/01/Damn-Cool-Algorithms-Fountain-Codes http://blog.notdot.net/2012/01/Damn-Cool-Algorithms-Fountain...
- shinratdr 14y agoHN formatting breaks the first Wikipedia link by removing the apostrophe. I ran it through a link shortener as a workaround. http://cl.ly/1r153b103k2P http://cl.ly/1r153b103k2P
- sadga 14y agoSomeone modified Wikipedia as a workaround.
- i_cannot_hack 14y agoOne could also replace the apostrophe with %27 http://en.wikipedia.org/wiki/Coupon_collector%27s_problem http://en.wikipedia.org/wiki/Coupon_collector%27s_problem
- skosuri 14y agoTo 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
- ipince 14y agoI'm sorry, can you clarify what that means? You wrote each piece of data 100 times? what does the 1000 refer to?
- skosuri 14y agowe printed the dna microarray using agilent's ink jet process (agilent is a spin off of hp; imagine an inkjet with actg instead of cmyk). each spot on the array has many hundreds of thousands of molecules. after we cleave the dna off the array, we take a portion of that, amplify and the sequence it. the portion we took off we estimate ~100 molecules for every oligo we made (55,000). we the sequence to get >55 million reads (so 1000x coverage); but these are just averages, and the distribution varies. you can check out the supplement of the paper if you are interested.
- somesaba 14y agoI think it refers to 1000x coverage on read which is then averaged