Mutually Uncorrelated Primers for DNA-Based Data Storage

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and for synchronization of communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized and cyclic codes.Comment: 14 pages, 3 figures, 1 Table. arXiv admin note: text overlap with arXiv:1601.0817

Lower Bounds on the Redundancy of Huffman Codes with Known and Unknown Probabilities

In this paper we provide a method to obtain tight lower bounds on the minimum redundancy achievable by a Huffman code when the probability distribution underlying an alphabet is only partially known. In particular, we address the case where the occurrence probabilities are unknown for some of the symbols in an alphabet. Bounds can be obtained for alphabets of a given size, for alphabets of up to a given size, and for alphabets of arbitrary size. The method operates on a Computer Algebra System, yielding closed-form numbers for all results. Finally, we show the potential of the proposed method to shed some light on the structure of the minimum redundancy achievable by the Huffman code