Achieving DNA Labeling Capacity with Minimum Labels through Extremal de Bruijn Subgraphs

Abstract: DNA labeling is a tool in molecular biology and biotechnology to visualize, detect, and study DNA at the molecular level. In this process, a DNA molecule is labeled by a set of specific patterns, referred to as labels, and is then imaged. The resulting image is modeled as an $(\ell+1)$-ary sequence, where $\ell$ is the number of labels, in which any non-zero symbol indicates the appearance of the corresponding label in the DNA molecule. The labeling capacity refers to the maximum information rate that can be achieved by the labeling process for any given set of labels. The main goal of this paper is to study the minimum number of labels of the same length required to achieve the maximum labeling capacity of 2 for DNA sequences or $\log_2q$ for an arbitrary alphabet of size $q$. The solution to this problem requires the study of path unique subgraphs of the de Bruijn graph with the largest number of edges. We provide upper and lower bounds on this value. We draw new connections to existing literature that let us prove an asymptotic result as the label length tends to infinity.