Search Results - Text Compression and Indexing Algorithms

Multidimensional query processing algorithm by dimension transformation by Rejwana Tasnim Rimi, K. M. Azharul Hasan, Tomohiro Tsuji

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Frequent contiguous pattern mining over biological sequences of protein misfolded diseases by Mohammad Tarequl Islam, Md. Abul Kashem Mia, Mohammad Shamsur Rahman, Mohammad Shamsul Arefin, Pranab Kumar Dhar, Takeshi Koshiba

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Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform by Cox, Anthony J., Bauer, Markus J., Jakobi, Tobias, Rosone, Giovanna

“…Motivation: The Burrows–Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing…”
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A linguistic steganography based on word indexing compression and candidate selection by Xiang, Lingyun, Wu, Wenshuai, Li, Xu, Yang, Chunfang

“… The length of the practical embedded payload can be reduced by the proposed word indexing compression algorithm(WIC…”
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Non-overlapping indexing in BWT-runs bounded space by Gibney, Daniel, MacNichol, Paul, Thankachan, Sharma V.

“…We revisit the non-overlapping indexing problem for an efficient repetition-aware solution…”
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Lightweight algorithms for constructing and inverting the BWT of string collections by Bauer, Markus J., Cox, Anthony J., Rosone, Giovanna

“… Such a dataset can now be generated in just a few days on a single sequencing machine. Many algorithms and data structures for compression and indexing of text have the BWT…”
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Foldcomp: a library and format for compressing and indexing large protein structure sets by Kim, Hyunbin, Mirdita, Milot, Steinegger, Martin

“…; these pose a challenge in terms of storage and processing. Here, we present Foldcomp, a novel lossy structure compression algorithm, and indexing system to address this challenge…”
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CREMSA : compressed indexing of (ultra) large multiple sequence alignments by Salson, Mikaël, Boddaert, Arthur, Gueye, Awa Bousso, Bulteau, Laurent, Hernandez--Courbevoie, Yohan, Marchet, Camille, Pan, Nan, Will, Sebastian, Ponty, Yann

“…). Such MSAs are largely ungapped, and mostly homogeneous on a column-wise level but not at a sequential level due to local variations, hindering the performances of sequential compression algorithms…”
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On compressing and indexing repetitive sequences by Kreft, Sebastian, Navarro, Gonzalo

“…We introduce LZ-End, a new member of the Lempel–Ziv family of text compressors, which achieves compression ratios close to those of LZ77 but is much faster at extracting arbitrary text substrings…”
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Stronger Lempel-Ziv Based Compressed Text Indexing by Arroyuelo, Diego, Navarro, Gonzalo, Sadakane, Kunihiko

“…Given a text T [1.. u ] over an alphabet of size σ , the full-text search problem consists in finding the occ occurrences of a given pattern P [1.. m…”
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Indexing k -mers in linear space for quality value compression by Shibuya, Yoshihiro, Comin, Matteo

“…Many bioinformatics tools heavily rely on -mer dictionaries to describe the composition of sequences and allow for faster reference-free algorithms or look-ups…”
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Efficient Compression and Indexing for Highly Repetitive DNA Sequence Collections by Huo, Hongwei, Chen, Xiaoyang, Guo, Xu, Vitter, Jeffrey Scott

“…In this paper, we focus upon the important problem of indexing and searching highly repetitive DNA sequence collections…”
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Fixed Block Compression Boosting in FM-Indexes: Theory and Practice by Gog, Simon, Kärkkäinen, Juha, Kempa, Dominik, Petri, Matthias, Puglisi, Simon J.

“… Our main theoretical result is a new technique called fixed block compression boosting , which is a simpler and faster alternative to optimal compression boosting and implicit compression boosting…”
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Resolution of the Burrows-Wheeler Transform Conjecture by Kempa, Dominik, Kociumaka, Tomasz

“… This is in contrast to nearly all other known compression methods, whose sizes have been shown to be either always within a \text{polylog}n factor…”
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Collapsing the Hierarchy of Compressed Data Structures: Suffix Arrays in Optimal Compressed Space by Kempa, Dominik, Kociumaka, Tomasz

“…The last two decades have witnessed a dramatic increase in the amount of highly repetitive datasets consisting of sequential data (strings, texts…”
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A new class of string transformations for compressed text indexing by Giancarlo, Raffaele, Manzini, Giovanni, Restivo, Antonio, Rosone, Giovanna, Sciortino, Marinella

“…Introduced about thirty years ago in the field of data compression, the Burrows-Wheeler Transform (BWT…”
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Geometric BWT: Compressed Text Indexing via Sparse Suffixes and Range Searching by Chien, Yu-Feng, Hon, Wing-Kai, Shah, Rahul, Thankachan, Sharma V., Vitter, Jeffrey Scott

“… This allows us to apply the lower bounds known in the field of orthogonal range searching to the problems in compressed text indexing…”
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On-Demand Indexing for Referential Compression of DNA Sequences by Alves, Fernando, Cogo, Vinicius, Wandelt, Sebastian, Leser, Ulf, Bessani, Alysson

“… Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evolutionary close species is exploited to reduce the storage demands…”
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Indexing labeled sequences by Rocher, Tatiana, Giraud, Mathieu, Salson, Mikaël

“…are a way to add some information on a text, such as functional annotations such as genes on a DNA sequences. V(D…”
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Compressed indexing and local alignment of DNA by Lam, T. W., Sung, W. K., Tam, S. L., Wong, C. K., Yiu, S. M.

“…). Without indexing, one can use dynamic programming to find all the local alignments between a text T and a pattern P in O(|T||P…”
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