相关论文: Hairpin Completion Distance Lower Bound

Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon…

Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…

Given a satisfiable 3-SAT formula, how hard is it to find an assignment to the variables that has Hamming distance at most n/2 to a satisfying assignment? More generally, consider any polynomial-time verifier for any NP-complete language. A…

We present an algorithm for approximating the edit distance between two strings of length $n$ in time $n^{1+\varepsilon}$ up to a constant factor, for any $\varepsilon>0$. Our result completes a research direction set forth in the recent…

A superstring of a set of strings correspond to a string which contains all the other strings as substrings. The problem of finding the Shortest Linear Superstring is a well-know and well-studied problem in stringology. We present here a…

In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…

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…

The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…

Given a set of pattern strings $\mathcal{P}=\{P_1, P_2,\ldots P_k\}$ and a text string $S$, the classic dictionary matching problem is to report all occurrences of each pattern in $S$. We study the dictionary problem in the compressed…

Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…

Let T be a triangulation of a simple polygon. A flip in T is the operation of removing one diagonal of T and adding a different one such that the resulting graph is again a triangulation. The flip distance between two triangulations is the…

We study the duplication with transposition distance between strings of length $n$ over a $q$-ary alphabet and their roots. In other words, we investigate the number of duplication operations of the form $x = (abcd) \to y = (abcbd)$, where…

The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…

In genome rearrangements, the mutational event transposition swaps two adjacent blocks of genes in one chromosome. The Transposition Distance Problem (TDP) aims to find the minimum number of transpositions required to transform one…

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…

Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…

The shift distance $\mathsf{sh}(S_1,S_2)$ between two strings $S_1$ and $S_2$ of the same length is defined as the minimum Hamming distance between $S_1$ and any rotation (cyclic shift) of $S_2$. We study the problem of sketching the shift…

Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…

Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…

Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…