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Stick graphs are intersection graphs of horizontal and vertical line segments that all touch a line of slope -1 and lie above this line. De Luca et al. [GD'18] considered the recognition problem of stick graphs when no order is given…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
We study the following fundamental realization problem of directed acyclic graphs (dags). Given a sequence S:=(a_1,b_1),...,(a_n, b_n) with a_i, b_i in Z_0^+, does there exist a dag (no parallel arcs allowed) with labeled vertex set V:=…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
Singleton arc consistency is an important type of local consistency which has been recently shown to solve all constraint satisfaction problems (CSPs) over constraint languages of bounded width. We aim to characterise all classes of CSPs…
We consider labeled directed graphs where each vertex is labeled with a non-empty string. Such labeled graphs are also known as non-linear texts in the literature. In this paper, we introduce a new problem of comparing two given labeled…
Consider two random strings having the same length and generated by an iid sequence taking its values uniformly in a fixed finite alphabet. Artificially place a long constant block into one of the strings, where a constant block is a…
This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including…
A repetition free Longest Common Subsequence (LCS) of two sequences x and y is an LCS of x and y where each symbol may appear at most once. Let R denote the length of a repetition free LCS of two sequences of n symbols each one chosen…
Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which…
A heapable sequence is a sequence of numbers that can be arranged in a "min-heap data structure". Finding a longest heapable subsequence of a given sequence was proposed by Byers, Heeringa, Mitzenmacher, and Zervas (ANALCO 2011) as a…
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
In this paper we show that the following problem is NP-complete: Given an alphabet $\Sigma$ and two strings over $\Sigma$, the question is whether there exists a permutation of $\Sigma$ which is a subsequence of both of the given strings.
Characterising tractable fragments of the constraint satisfaction problem (CSP) is an important challenge in theoretical computer science and artificial intelligence. Forbidding patterns (generic sub-instances) provides a means of defining…
Classic symmetry-breaking problems on graphs have gained a lot of attention in models of modern parallel computation. The Adaptive Massively Parallel Computation (AMPC) is a model that captures the central challenges in data center…
The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…
In this paper, we study for the first time the Diverse Longest Common Subsequences (LCSs) problem under Hamming distance. Given a set of a constant number of input strings, the problem asks to decide if there exists some subset $\mathcal X$…
The Longest Common Subsequence (LCS) Problem asks for the longest sequence of (non-contiguous) matches between two given strings of characters. Using extensive Monte Carlo simulations, we find a finite size scaling law of the form E(L)/N =C…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…