相关论文: On Critical Relative Distance of DNA Codes for Add…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
This paper considers cyclic DNA codes of arbitrary length over the ring $R=\F_2[u]/u^4-1$. A mapping is given between the elements of $R$ and the alphabet $\{A,C,G,T\}$ which allows the additive stem distance to be extended to this ring.…
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…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a…
In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
Mutual correlation between segments of DNA or protein sequences can be detected by Smith-Waterman local alignments. We present a statistical analysis of alignment of such sequences, based on a recent scaling theory. A new fidelity measure…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
We study the problem of approximating a discrete probability distribution, such as the next-token distribution of a large language model, by a dyadic distribution induced by a binary tree under encoding rate constraints. The objective is to…