57 research outputs found
Codes Correcting Two Deletions
In this work, we investigate the problem of constructing codes capable of
correcting two deletions. In particular, we construct a code that requires
redundancy approximately 8 log n + O(log log n) bits of redundancy, where n is
the length of the code. To the best of the author's knowledge, this represents
the best known construction in that it requires the lowest number of redundant
bits for a code correcting two deletions
Asymmetric Lee Distance Codes for DNA-Based Storage
We consider a new family of codes, termed asymmetric Lee distance codes, that
arise in the design and implementation of DNA-based storage systems and systems
with parallel string transmission protocols. The codewords are defined over a
quaternary alphabet, although the results carry over to other alphabet sizes;
furthermore, symbol confusability is dictated by their underlying binary
representation. Our contributions are two-fold. First, we demonstrate that the
new distance represents a linear combination of the Lee and Hamming distance
and derive upper bounds on the size of the codes under this metric based on
linear programming techniques. Second, we propose a number of code
constructions which imply lower bounds
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
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