Related papers: Palindromic Decompositions with Gaps and Errors
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
The $k$-mismatch problem consists in computing the Hamming distance between a pattern $P$ of length $m$ and every length-$m$ substring of a text $T$ of length $n$, if this distance is no more than $k$. In many real-world applications, any…
We present a method which displays all palindromes of a given length from De Bruijn words of a certain order, and also a recursive one which constructs all palindromes of length $n+1$ from the set of palindromes of length $n$. We show that…
Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length $n$ over a fixed alphabet…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
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…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
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…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
Benders decomposition is a widely used method for solving large optimization problems, but its performance is often hindered by the repeated solution of subproblems. We propose a flexible and modular algorithmic framework for accelerating…
In the beautifully simple-to-state problem of trace reconstruction, the goal is to reconstruct an unknown binary string $x$ given random "traces" of $x$ where each trace is generated by deleting each coordinate of $x$ independently with…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
Statistical design of experiments is widely used in scientific and industrial investigations. A generalized minimum aberration (GMA) orthogonal array is optimum under the well-established, so-called GMA criterion, and such an array can…
In the $k$-mismatch problem we are given a pattern of length $n$ and a text and must find all locations where the Hamming distance between the pattern and the text is at most $k$. A series of recent breakthroughs have resulted in an…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
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…
Detectability of failures of linear programming (LP) decoding and the potential for improvement by adding new constraints motivate the use of an adaptive approach in selecting the constraints for the underlying LP problem. In this paper, we…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
We consider the distributed and parallel construction of low-diameter decompositions with strong diameter for (weighted) graphs and (weighted) graphs that can be separated through $k \in \tilde{O}(1)$ shortest paths. This class of graphs…