Related papers: Hybrid Indexes for Repetitive Datasets
For decades, computing the LZ factorization (or LZ77 parsing) of a string has been a requisite and computationally intensive step in many diverse applications, including text indexing and data compression. Many algorithms for LZ77 parsing…
Compression techniques that support fast random access are a core component of any information system. Current state-of-the-art methods group documents into fixed-sized blocks and compress each block with a general-purpose adaptive…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
A search query consists of several words. In a proximity full-text search, we want to find documents that contain these words near each other. This task requires much time when the query consists of high-frequently occurring words. If we…
The Suffix Array is a classic text index enabling on-line pattern matching queries via simple binary search. The main drawback of the Suffix Array is that it takes linear space in the text's length, even if the text itself is extremely…
We describe indexes for searching large data sets for variable-length-gapped (VLG) patterns. VLG patterns are composed of two or more subpatterns, between each adjacent pair of which is a gap-constraint specifying upper and lower bounds on…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
The importance of an efficient and scalable document similarity detection system is undeniable nowadays. Search engines need batch text similarity measures to detect duplicated and near-duplicated web pages in their indexes in order to…
We propose an unsupervised hashing method which aims to produce binary codes that preserve the ranking induced by a real-valued representation. Such compact hash codes enable the complete elimination of real-valued feature storage and allow…
Compressed indexing enables powerful queries over massive and repetitive textual datasets using space proportional to the compressed input. While theoretical advances have led to highly efficient index structures, their practical…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
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 $T$…
While several self-indexes for highly repetitive texts exist, developing a practical self-index applicable to real world repetitive texts remains a challenge. ESP-index is a grammar-based self-index on the notion of edit-sensitive parsing…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
Gagie, Navarro and Prezza's $r$-index (SODA, 2018) promises to speed up DNA alignment and variation calling by allowing us to index entire genomic databases, provided certain obstacles can be overcome. In this paper we first strengthen and…