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

Optimal Linear and Cyclic Locally Repairable Codes over Small Fields

We consider locally repairable codes over small fields and propose constructions of optimal cyclic and linear codes in terms of the dimension for a given distance and length. Four new constructions of optimal linear codes over small fields with locality properties are developed. The first two approaches give binary cyclic codes with locality two. While the first construction has availability one, the second binary code is characterized by multiple available repair sets based on a binary Simplex code. The third approach extends the first one to q-ary cyclic codes including (binary) extension fields, where the locality property is determined by the properties of a shortened first-order Reed-Muller code. Non-cyclic optimal binary linear codes with locality greater than two are obtained by the fourth construction.Comment: IEEE Information Theory Workshop (ITW) 2015, Apr 2015, Jerusalem, Israe