Related papers: Extending the Burrows-Wheeler Transform for Cartes…
Many websites with an underlying database containing structured data provide the richest and most dense source of information relevant for topical data integration. The real data integration requires sustainable and reliable pattern…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
We revisit the complexity of building, given a two-dimensional string of size $n$, an indexing structure that allows locating all $k$ occurrences of a two-dimensional pattern of size $m$. While a structure of size $\mathcal{O}(n)$ with…
The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the…
The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…
The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
Space-filling curves (SFC, for short) have been widely applied to index multi-dimensional data, which first maps the data to one dimension, and then a one-dimensional indexing method, e.g., the B-tree indexes the mapped data. Existing SFCs…
We present a new semi-external algorithm that builds the Burrows--Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression techniques to reduce computational costs when the input is…
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…
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
Representing the movements of objects (trips) over a network in a compact way while retaining the capability of exploiting such data effectively is an important challenge of real applications. We present a new Compact Trip Representation…