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DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization affinities (or stabilities) of perfect double helix constructed by individual single-stranded DNA (ssDNA) and its RC pair, we propose a novel similarity significance (SS) model to measure the similarity between DNA sequences. Particularly, instead of directly measuring the similarity of two sequences by any metric/approach, the proposed SS works in a way to evaluate how more likely will the undesirable hybridizations occur over the desirable hybridizations in the presence of the two measured sequences and their RC pairs. With this SS model, we construct thermodynamically stable DNA codes subject to several combinatorial constraints using a sorting-based algorithm. The proposed scheme results in DNA codes with larger code sizes and wider free energy gaps (hence better cross-hybridization performance) compared to the existing methods.
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the hybridization potential of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a thermodynamica
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very ofte
This paper focuses on controlling the absorbing set spectrum for a class of regular LDPC codes known as separable, circulant-based (SCB) codes. For a specified circulant matrix, SCB codes all share a common mother matrix, examples of which are array-
This work addresses the physical layer channel code design for an uncoordinated, frame- and slot-asynchronous random access protocol. Starting from the observation that collisions between two users yield very specific interference patterns, we define
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this melting transition have been intensively investigated. Recently t