Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging task. This paper aims to address simultaneously correcting two types of errors, namely, short tandem duplication and substitution errors. We focus on tandem repeats of length at most 3 and design codes for correcting an arbitrary number of duplication errors and one substitution error. Because a substituted symbol can be duplicated many times (as part of substrings of various lengths), a single substitution can affect an unbounded substring of the retrieved word. However, we show that with appropriate preprocessing, the effect may be limited to a substring of finite length, thus making efficient error-correction possible. We construct a code for correcting the aforementioned errors and provide lower bounds for its rate. Compared to optimal codes correcting only duplication errors, numerical results show that the asymptotic cost of protecting against an additional substitution is only 0.003 bits/symbol when the alphabet has size 4, an important case corresponding to data storage in DNA.
In this work, we derive upper bounds on the cardinality of tandem duplication and palindromic deletion correcting codes by deriving the generalized sphere packing bound for these error types. We first prove that an upper bound for tandem deletions is also an upper bound for inserting the respective type of duplications. Therefore, we derive the bounds based on these special deletions as this results in tighter bounds. We determine the spheres for tandem and palindromic duplications/deletions and the number of words with a specific sphere size. Our upper bounds on the cardinality directly imply…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem duplications. Known code constructions are based on {\em irreducible words}. We study efficient encoding/decoding methods for irreducible words. First, we describe an $(\ell,m)$-finite state encoder and show that when $m=Θ(1/ε)$ and $\ell=Θ(1/ε)$, the encoder achieves rate that is $ε$ away from the optimal. Next, we provide ranking/unranking algorithms for ir…
In this work, we propose constructions that correct duplications of multiple consecutive symbols. These errors are known as tandem duplications, where a sequence of symbols is repeated; respectively as palindromic duplications, where a sequence is repeated in reversed order. We compare the redundancies of these constructions with code size upper bounds that are obtained from sphere packing arguments. Proving that an upper bound on the code cardinality for tandem deletions is also an upper bound for inserting tandem duplications, we derive the bounds based on this special tandem deletion error …
In this paper, we study codes correcting $t$ duplications of $\ell$ consecutive symbols. These errors are known as tandem duplication errors, where a sequence of symbols is repeated and inserted directly after its original occurrence. Using sphere packing arguments, we derive non-asymptotic upper bounds on the cardinality of codes that correct such errors for any choice of parameters. Based on the fact that a code correcting insertions of $t$ zero-blocks can be used to correct $t$ tandem duplications, we construct codes for tandem duplication errors. We compare the cardinalities of these codes…
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 pres…
We propose a list-decoding scheme for reconstruction codes in the context of uniform-tandem-duplication noise, which can be viewed as an application of the associative memory model to this setting. We find the uncertainty associated with $m>2$ strings (where a previous paper considered $m=2$) in asymptotic terms, where code-words are taken from an error-correcting code. Thus, we find the trade-off between the design minimum distance, the number of errors, the acceptable list size and the resulting uncertainty, which corresponds to the required number of distinct retrieved outputs for successfu…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction problem, which is applicable whenever multiple reads of noisy data are available. This strategy is uniquely suited to the medium, which inherently replicates stored data in multiple distinct ways, caused by mutations. We consider noise introduced solely by uniform tandem-duplication, and utilize the relation to constant-weight integer codes in the Manhattan metri…
The set of all $ q $-ary strings that do not contain repeated substrings of length $ \leqslant\! 3 $ (i.e., that do not contain substrings of the form $ a a $, $ a b a b $, and $ a b c a b c $) constitutes a code correcting an arbitrary number of tandem-duplication mutations of length $ \leqslant\! 3 $. In other words, any two such strings are non-confusable in the sense that they cannot produce the same string while evolving under tandem duplications of length $ \leqslant\! 3 $. We demonstrate that this code is asymptotically optimal in terms of rate, meaning that it represents the largest se…
The majority of the human genome consists of repeated sequences. An important type of repeated sequences common in the human genome are tandem repeats, where identical copies appear next to each other. For example, in the sequence $AGTC\underline{TGTG}C$, $TGTG$ is a tandem repeat, that may be generated from $AGTCTGC$ by a tandem duplication of length $2$. In this work, we investigate the possibility of generating a large number of sequences from a \textit{seed}, i.e.\ a small initial string, by tandem duplications of bounded length. We study the capacity of such a system, a notion that quanti…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in which the substitutions occur only within the duplicated substrings, and one in which the location of substitutions is unrestricted. Both error-detecting and error-correcting codes are constructed, which can handle correctly any number of tandem duplications of a fixed length $k$, and at most a single substitution occurring at any time during the mutation pro…
We study the tandem duplication distance between binary sequences and their roots. In other words, the quantity of interest is the number of tandem duplication operations of the form $\seq x = \seq a \seq b \seq c \to \seq y = \seq a \seq b \seq b \seq c$, where $\seq x$ and $\seq y$ are sequences and $\seq a$, $\seq b$, and $\seq c$ are their substrings, needed to generate a binary sequence of length $n$ starting from a square-free sequence from the set $\{0,1,01,10,010,101\}$. This problem is a restricted case of finding the duplication/deduplication distance between two sequences, defined a…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data, e.g., estimation of model parameters and compression. At the same time, due to the complexity of these processes, designing tractable stochastic models and analyzing them are challenging. In this paper, we study two kinds of systems, each representing a set of mutations. In the first system, tandem duplications and substitution mutations are allowed and in th…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions, duplications, and substitutions may arise in DNA at different stages of data storage and retrieval. The current paper constructs error-correcting codes for simultaneously correcting short (tandem) duplications and at most $p$ edits, where a short duplication generates a copy of a substring with length $\leq 3$ and inserts the copy following the original substri…
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 a 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. An exact duplication inserts a copy of a substring of length k of the sequence immediately after that substring, e.g., ACGT to ACGACGT, where k = 3, while a noisy d…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by interleaving watermark and periodic marker signals; conversion from binary to ternary, quaternary or mixed-radix sequences via an efficient block code; encoding into a DNA sequence that avoids homopolymer, dinucleotide, or trinucleotide runs and other short local repeats; and detection/correction of errors (including local duplications, burst deletions, and sub…
This paper is concerned with the problem of error-free communication over the i.i.d. duplication channel which acts on a transmitted sequence $ x_1 \cdots x_n $ by inserting a random number of copies of each symbol $ x_i $ next to the original symbol. The random variables representing the numbers of inserted copies at each position $ i $ are independent and take values in $ \{0, 1, \ldots, r\} $, where $ r $ is a fixed parameter. A more general model in which blocks of $ \ell $ consecutive symbols are being duplicated, and which is inspired by DNA-based data storage systems wherein the stored …
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of synchronization errors, as well as in several information storage applications. We demonstrate that Levenshtein's construction of binary codes correcting insertions of zeros is, with minor modifications, applicable also to channels with arbitrary alphabets and with duplication errors of arbitrary (but fixed) length $ k $. Furthermore, we derive bounds on the cardi…
Tandem-duplication-random-loss (TDRL) is an important genome rearrangement operation studied in evolutionary biology. This paper investigates some of the formal properties of TDRL operations on the symmetric group (the space of permutations over an $ n $-set). In particular, the cardinality of `balls' of radius one in the TDRL metric, as well as the cardinality of the maximum intersection of two such balls, are determined. The corresponding problems for the so-called mirror (or palindromic) TDRL rearrangement operations are also solved. The results represent an initial step in the study of err…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in relation to the code's minimum distance. We also devise efficient reconstruction algorithms for various limited-magnitude error parameter ranges. We then extend these algorithms to the list-reconstruction scheme, and show the trade-off between the asymptotic list size and the number of required channel outputs. These results apply to all codes, without any assump…
