Related papers: The Longest Run Subsequence Problem: Further Compl…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
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,…
Kernelization is an important tool in parameterized algorithmics. Given an input instance accompanied by a parameter, the goal is to compute in polynomial time an equivalent instance of the same problem such that the size of the reduced…
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…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Lately, there is a growing interest in dynamic string matching problems. Specifically, the dynamic Longest Common Factor problem has been researched and some interesting results has been reached. In this paper we examine another classic…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
In this paper we propose a new framework for analyzing the performance of preprocessing algorithms. Our framework builds on the notion of kernelization from parameterized complexity. However, as opposed to the original notion of…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
Tracking of moving objects is crucial to security systems and networks. Given a graph $G$, terminal vertices $s$ and $t$, and an integer $k$, the \textsc{Tracking Paths} problem asks whether there exists at most $k$ vertices, which if…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
A border of a string is a non-empty proper prefix of the string that is also a suffix. A string is unbordered if it has no border. The longest unbordered factor is a fundamental notion in stringology, closely related to string periodicity.…
The Shortest Common Supersequence problem (SCS for short) consists in finding a shortest common supersequence of a finite set of words on a fixed alphabet Sigma. It is well-known that its decision version denoted [SR8] in [Garey and…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
One of the central problems in the classification of individual test sequences (e.g. genetic analysis), is that of checking for the similarity of sample test sequences as compared with a set of much longer training sequences. This is done…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…