[troymc]

It sounds like they are reading several DNA strands in parallel at the same time, and each output-sequence has noise. It seems to me the problem then becomes one of finding the most probable "signal sequence" given all those noisy output-sequences. Oh, and it also sounds like you wouldn't know which letter is number 1, which is number 2, etc. Is that right?

It seems like a fun problem in information theory. Can you point us to some articles or papers about current approaches to solving it?

[waiquoo]

Winston Timp has done some interesting work in this area (http://www.sciencedirect.com/science/article/pii/S0006349512...). Basically, by training a hidden Markov Model, you can get the most likely sequence from a noisy source.