Error-correcting Codes for Noisy Duplication Channels

Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to wider range of errors resulting from various processes involved in the data storage...

Full description

Saved in:
Bibliographic Details
Published in2019 57th Annual Allerton Conference on Communication, Control, and Computing (Allerton) pp. 140 - 146
Main Authors Tang, Yuanyuan, Farnoud, Farzad
Format Conference Proceeding
LanguageEnglish
Published IEEE 01.09.2019
Subjects
DNA
Error correction
Error correction codes
Hamming distance
Media
Memory
Noise measurement
Online AccessGet full text

Cover

More Information
Summary:Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to wider range of errors resulting from various processes involved in the data storage pipeline. In this paper, we consider correcting duplication errors for both exact and noisy tandem duplications of a given length k. Specifically, we design codes that can correct any number of exact duplication and one noisy duplication errors, where in the noisy duplication case the copy is at Hamming distance 1 from the original. Our constructions rely upon recovering the duplication root of the stored codeword. We characterize the ways in which duplication errors manifest in the root of affected sequences and design efficient codes for correcting these error patterns. We show that the proposed construction is asymptotically optimal.
DOI:10.1109/ALLERTON.2019.8919847