Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms

The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors arising from various mutations, such as point mutations, indels, and tandem duplication, which need to be corrected to maintain data integrity. In this paper, we provide error-correcting codes for errors caused by tandem duplications, which create a copy of a block of the sequence and insert it in a tandem manner, i.e., next to the original. In particular, we present a family of codes for correcting errors due to tandem-duplications of a fixed length and any number of errors. We also study codes for correcting tandem duplications of length up to a given constant $k$, where we are primarily focused on the cases of $k=2,3$.