Related papers: Palindromic Decompositions with Gaps and Errors
We consider the problem of recognizing a vocabulary--a collection of words (sequences) over a finite alphabet--from a potential subsequence of one of its words. We assume the given subsequence is received through a deletion channel as a…
Pattern matching can be used to calculate the support of patterns, and is a key issue in sequential pattern mining (or sequence pattern mining). Nonoverlapping pattern matching means that two occurrences cannot use the same character in the…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
In this work, we address the problem of approximate pattern matching with wildcards. Given a pattern $P$ of length $m$ containing $D$ wildcards, a text $T$ of length $n$, and an integer $k$, our objective is to identify all fragments of $T$…
Following (Kolpakov et al., 2013; Gawrychowski and Manea, 2015), we continue the study of {\em $\alpha$-gapped repeats} in strings, defined as factors $uvu$ with $|uv|\leq \alpha |u|$. Our main result is the $O(\alpha n)$ bound on the…
We show that the number of all maximal $\alpha$-gapped repeats and palindromes of a word of length $n$ is at most $3(\pi^2/6 + 5/2) \alpha n$ and $7 (\pi^2 / 6 + 1/2) \alpha n - 5 n - 1$, respectively.
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…
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…
We prove a precise formula for the minimal number K(n) such that every binary word of length $n$ can be divided into K(n) palindromes. Also we estimate the average number $\ol K(n)$ of palindromes composing a random binary word of the…
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…
The palindrome pattern matching (pal-matching) is a kind of generalized pattern matching, in which two strings $x$ and $y$ of same length are considered to match (pal-match) if they have the same palindromic structures, i.e., for any…
Given a string $s$ of length $n$ over a general alphabet and an integer $k$, the problem is to decide whether $s$ is a concatenation of $k$ nonempty palindromes. Two previously known solutions for this problem work in time $O(kn)$ and…
We study the online variant of the language distance problem for two classical formal languages, the language of palindromes and the language of squares, and for the two most fundamental distances, the Hamming distance and the edit…
In the Palindrome Problem one tries to find all palindromes (palindromic substrings) in a given string. A palindrome is defined as a string which reads forwards the same as backwards, e.g., the string "racecar". A related problem is the…
A gapped repeat is a factor of the form $uvu$ where $u$ and $v$ are nonempty words. The period of the gapped repeat is defined as $|u|+|v|$. The gapped repeat is maximal if it cannot be extended to the left or to the right by at least one…
In the problem of $\texttt{Generalised Pattern Matching}\ (\texttt{GPM})$ [STOC'94, Muthukrishnan and Palem], we are given a text $T$ of length $n$ over an alphabet $\Sigma_T$, a pattern $P$ of length $m$ over an alphabet $\Sigma_P$, and a…
A palindromic substring $T[i.. j]$ of a string $T$ is said to be a shortest unique palindromic substring (SUPS) in $T$ for an interval $[p, q]$ if $T[i.. j]$ is a shortest palindromic substring such that $T[i.. j]$ occurs only once in $T$,…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for…
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…