Related papers: MONI can find k-MEMs
We show a theorem on monadic second-order k-ary queries on finite words. It may be illustrated by the following example: if the number of results of a query on binary strings is O(number of 0s $\times$ number of 1s), then each result can be…
We consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size $N$ over alphabet $[1,\sigma]$ is composed of $D$ copies…
An optimal index solving top-k document retrieval [Navarro and Nekrich, SODA12] takes O(m + k) time for a pattern of length m, but its space is at least 80n bytes for a collection of n symbols. We reduce it to 1.5n to 3n bytes, with…
In the $k$-Edit Circular Pattern Matching ($k$-Edit CPM) problem, we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a positive integer threshold $k$, and we are to report all starting positions of the substrings of $T$ that…
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…
A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…
We introduce data structures answering queries concerning the occurrences of patterns from a given dictionary $\mathcal{D}$ in fragments of a given string $T$ of length $n$. The dictionary is internal in the sense that each pattern in…
We introduce a compressed suffix array representation that, on a text $T$ of length $n$ over an alphabet of size $\sigma$, can be built in $O(n)$ deterministic time, within $O(n\log\sigma)$ bits of working space, and counts the number of…
The $r$-index (Gagie et al., JACM 2020) represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude. Its space usage, $\mathcal{O}(r)$ where $r$ is the number of…
The text-to-pattern Hamming distances problem asks to compute the Hamming distances between a given pattern of length $m$ and all length-$m$ substrings of a given text of length $n\ge m$. We focus on the $k$-mismatch version of the problem,…
The Burrows Wheeler transform has applications in data compression as well as full text indexing. Despite its important applications and various existing algorithmic approaches the construction of the transform for large data sets is still…
Let two static sequences of strings $P$ and $S$, representing prefix and suffix conditions respectively, be given as input for preprocessing. For the query, let two positive integers $k_1$ and $k_2$ be given, as well as a string $T$ given…
We show that for any set of $n$ points moving along "simple" trajectories (i.e., each coordinate is described with a polynomial of bounded degree) in $\Re^d$ and any parameter $2 \le k \le n$, one can select a fixed non-empty subset of the…
Let $S_{T}(k)$ denote the set of distinct substrings of length $k$ in a string $T$, then the $k$-th substring complexity is defined by its cardinality $|S_{T}(k)|$. Recently, $\delta = \max \{ |S_{T}(k)| / k : k \ge 1 \}$ is shown to be a…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
Permutation $\sigma$ appears in permutation $\pi$ if there exists a subsequence of $\pi$ that is order-isomorphic to $\sigma$. The natural question is to check if $\sigma$ appears in $\pi$, and if so count the number of occurrences. We know…
Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…