Optimizing the Decoding Probability and Coverage Ratio of Composite DNA

Abstract

This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm, every composite symbols does not store a single nucleotide but a mixture of the four DNA nucleotides. The first problem studies the expected number of strand reads in order to decode a composite strand or a group of composite strands. In the second problem, our goal is study how to carefully choose a fixed number of mixtures of the DNA nucleotides such that the decoding probability by the maximum likelihood decoder is maximized.