1 research outputs found
Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly
<i>De novo</i> DNA synthesis is in need of new ideas
for increasing production rate and reducing cost. DNA reuse in combinatorial
library construction is one such idea. Here, we describe an algorithm
for planning multistage assembly of DNA libraries with shared intermediates
that greedily attempts to maximize DNA reuse, and show both theoretically
and empirically that it runs in linear time. We compare solution quality
and algorithmic performance to the best results reported for computing
DNA assembly graphs, finding that our algorithm achieves solutions
of equivalent quality but with dramatically shorter running times
and substantially improved scalability. We also show that the related
computational problem <i>bounded-depth min-cost string production</i> (BDMSP), which captures DNA library assembly operations with a simplified
cost model, is NP-hard and APX-hard by reduction from vertex cover.
The algorithm presented here provides solutions of near-minimal stages
and thanks to almost instantaneous planning of DNA libraries it can
be used as a metric of ″manufacturability″ to guide
DNA library design. Rapid planning remains applicable even for DNA
library sizes vastly exceeding today’s biochemical assembly
methods, future-proofing our method