Related papers: Lectures on DNA Codes
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
The classical family of $[n,k]_q$ Reed-Solomon codes over a field $\F_q$ consist of the evaluations of polynomials $f \in \F_q[X]$ of degree $< k$ at $n$ distinct field elements. In this work, we consider a closely related family of codes,…
In this paper we prove new lower bounds for the maximal size of permutation codes by connecting the theory of permutation codes with the theory of linear block codes. More specifically, using the columns of a parity check matrix of an…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
This paper presents a new approach for code similarity on High Level programs. Our technique is based on Fast Dynamic Time Warping, that builds a warp path or points relation with local restrictions. The source code is represented into Time…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
Similarity functions measure how comparable pairs of elements are, and play a key role in a wide variety of applications, e.g., notions of Individual Fairness abiding by the seminal paradigm of Dwork et al., as well as Clustering problems.…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
The length function $\ell_q(r,R)$ is the smallest length of a $q$-ary linear code of codimension (redundancy) $r$ and covering radius $R$. The $d$-length function $\ell_q(r,R,d)$ is the smallest length of a $q$-ary linear code with…
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…
The coding and noncoding length sequences constructed from a complete genome are characterised by multifractal analysis. The dimension spectrum $D_{q}$ and its derivative, the 'analogous' specific heat $C_{q}$, are calculated for the coding…
In this work we implement the so-called matching time estimators for estimating the entropy rate as well as the entropy production rate for symbolic sequences. These estimators are based on recurrence properties of the system, which have…