Related papers: Deterministic Polynomial-Time Algorithms for Desig…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
A randomized algorithm for a search problem is *pseudodeterministic* if it produces a fixed canonical solution to the search problem with high probability. In their seminal work on the topic, Gat and Goldwasser posed as their main open…
A $c$-short program for a string $x$ is a description of $x$ of length at most $C(x) + c$, where $C(x)$ is the Kolmogorov complexity of $x$. We show that there exists a randomized algorithm that constructs a list of $n$ elements that…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
In recent years, several powerful techniques have been developed to design {\em randomized} polynomial-space parameterized algorithms. In this paper, we introduce an enhancement of color coding to design deterministic polynomial-space…
Tandem duplication in DNA 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 {\em et al.} (2016) proposed the study of codes that…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
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…
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
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…
We present new deterministic algorithms for several cases of the maximum rank matrix completion problem (for short matrix completion), i.e. the problem of assigning values to the variables in a given symbolic matrix as to maximize the…
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…
We provide the first fully polynomial-time randomized approximation scheme for the following two counting problems: 1. Given a Context Free Grammar $G$ over alphabet $\Sigma$, count the number of words of length exactly $n$ generated by…
We study the problems of finding a shortest synchronizing word and its length for a given prefix code. This is done in two different settings: when the code is defined by an arbitrary decoder recognizing its star and when the code is…
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
We show that Reed-Solomon codes of dimension $k$ and block length $n$ over any finite field $\mathbb{F}$ can be deterministically list decoded from agreement $\sqrt{(k-1)n}$ in time $\text{poly}(n, \log |\mathbb{F}|)$. Prior to this work,…
We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
Schoening presents a simple randomized algorithm for (d,k)-CSP problems with running time (d(k-1)/k)^n poly(n). Here, d is the number of colors, k is the size of the constraints, and n is the number of variables. A derandomized version of…