Related papers: Efficient pattern matching in degenerate strings w…
A degenerate symbol x* over an alphabet A is a non-empty subset of A, and a sequence of such symbols is a degenerate string. A degenerate string is said to be conservative if its number of non-solid symbols is upper-bounded by a fixed…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
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…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
It is widely assumed that $O(m+\lg \sigma)$ is the best one can do for finding a pattern of length $m$ in a compacted trie storing strings over an alphabet of size $\sigma$, if one insists on linear-size data structures and deterministic…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
Burrows-Wheeler transform (BWT) is an invertible text transformation that, given a text $T$ of length $n$, permutes its symbols according to the lexicographic order of suffixes of $T$. BWT is one of the most heavily studied algorithms in…
Given a string of characters, the Burrows-Wheeler Transform rearranges the characters in it so as to produce another string of the same length which is more amenable to compression techniques such as move to front, run-length encoding, and…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
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…
Introduced about thirty years ago in the field of Data Compression, the Burrows-Wheeler Transform (BWT) is a string transformation that, besides being a booster of the performance of memoryless compressors, plays a fundamental role in the…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
The Burrows-Wheeler transform (BWT) is a well studied text transformation widely used in data compression and text indexing. The BWT of two strings can also provide similarity measures between them, based on the observation that the more…
Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which…