Related papers: Faster STR-EC-LCS Computation

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…

In the Manhattan Sequence Consensus problem (MSC problem) we are given $k$ integer sequences, each of length $l$, and we are to find an integer sequence $x$ of length $l$ (called a consensus sequence), such that the maximum Manhattan…

The recently introduced longest common substring with $k$-mismatches ($k$-LCF) problem is to find, given two sequences $S_1$ and $S_2$ of length $n$ each, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance…

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…

Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are…

The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…

Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…

Two important similarity measures between sequences are the longest common subsequence (LCS) and the dynamic time warping distance (DTWD). The computations of these measures for two given sequences are central tasks in a variety of…

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…

We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the…

In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…

This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…

The longest common substring with $k$-mismatches problem is to find, given two strings $S_1$ and $S_2$, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance between $A_1$ and $A_2$ is $\le k$. We introduce a…

In this paper we address the longest common extension (LCE) problem: to compute the length $\ell$ of the longest common prefix between any two suffixes of $T\in \Sigma^n$ with $ \Sigma = \{0, \ldots \sigma-1\} $. We present two fast and…

An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…

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…

Let $X_1, X_2, ..., X_s$ and $Y_1, Y_2, ..., Y_t$ be strings over an alphabet $\Sigma$, where $s$ and $t$ are positive integers. The longest common subsequence and substring problem for multiple strings $X_1, X_2, ..., X_s$ and $Y_1, Y_2,…

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…

We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…

In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…