Results 21 to 30 of about 14,384 (164)
Accelerated preprocessing in task of searching substrings in a string
Advanced Engineering Research, 2019 Introduction. A rapid development of the systems such as Yandex, Google, etc., has predetermined the relevance of the task of searching substrings in a string, and approaches to its solution are actively investigated. This task is used to create database
A. V. Mazurenko, N. V. Boldyrikhin
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These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure. [PDF]
PLoS ONE, 2014 K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation.
Qingpeng Zhang +4 more
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On the suitability of suffix arrays for lempel-ziv data compression [PDF]
, 2009 Lossless compression algorithms of the Lempel-Ziv (LZ) family are widely used nowadays. Regarding time and memory requirements, LZ encoding is much more demanding than decoding.
D. Gusfield +9 more
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Gclust: A Parallel Clustering Tool for Microbial Genomic Data
Genomics, Proteomics & Bioinformatics, 2019 The accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources. Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering ...
Ruilin Li +17 more
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Computing Maximal Lyndon Substrings of a String
Algorithms, 2020 There are two reasons to have an efficient algorithm for identifying all right-maximal Lyndon substrings of a string: firstly, Bannai et al. introduced in 2015 a linear algorithm to compute all runs of a string that relies on knowing all right-maximal ...
Frantisek Franek, Michael Liut
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Compressed Representations of Permutations, and Applications [PDF]
, 2008 We explore various techniques to compress a permutation $\pi$ over n integers, taking advantage of ordered subsequences in $\pi$, while supporting its application $\pi$(i) and the application of its inverse $\pi^{-1}(i)$ in small time.
Barbay, Jérémy, Navarro, Gonzalo
core +7 more sources
Approximate String Matching with Compressed Indexes
Algorithms, 2009 A compressed full-text self-index for a text T is a data structure requiring reduced space and able to search for patterns P in T. It can also reproduce any substring of T, thus actually replacing T. Despite the recent explosion of interest on compressed
Pedro Morales +3 more
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Lyndon Array Construction during Burrows-Wheeler Inversion [PDF]
, 2017 In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$.
Louza, Felipe A. +3 more
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Deterministic sub-linear space LCE data structures with efficient construction [PDF]
, 2016 Given a string $S$ of $n$ symbols, a longest common extension query $\mathsf{LCE}(i,j)$ asks for the length of the longest common prefix of the $i$th and $j$th suffixes of $S$. LCE queries have several important applications in string processing, perhaps
Bannai, Hideo +5 more
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EERTREE: An Efficient Data Structure for Processing Palindromes in Strings [PDF]
, 2015 We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using this structure,
Rubinchik, Mikhail, Shur, Arseny M.
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