gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections
Algorithms for Molecular Biology, 2020 Background The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings.
Felipe A. Louza +4 more
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Compression and information entropy of binary strings from the collision history of three hard balls
Journal of Physics Communications, 2023 We investigate how to measure and define the entropy of a simple chaotic system, three hard spheres on a ring. A novel approach is presented, which does not assume the ergodic hypothesis.
M Vedak, G J Ackland
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Calculating Kolmogorov complexity from the output frequency distributions of small Turing machines. [PDF]
PLoS ONE, 2014 Drawing on various notions from theoretical computer science, we present a novel numerical approach, motivated by the notion of algorithmic probability, to the problem of approximating the Kolmogorov-Chaitin complexity of short strings.
Fernando Soler-Toscano +3 more
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Linear space string correction algorithm using the Damerau-Levenshtein distance
BMC Bioinformatics, 2020 Background The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion,
Chunchun Zhao, Sartaj Sahni
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Efficient and effectiveness retrieval of information using some of the approximate string matching algorithms [PDF]
مجلة التربية والعلم, 2008 The research aims at buliding integral computer database for sales ,by using six algorithms of approximate string matching with practicable example;soundex,information metaphone,longest common subsequence ,dice cofficient,levenshtein distance and fuzzy ...
Anhar Mohammed, Suhiar Essa
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Permuted Pattern Matching Algorithms on Multi-Track Strings
Algorithms, 2019 A multi-track string is a tuple of strings of the same length. Given the pattern and text of two multi-track strings, the permuted pattern matching problem is to find the occurrence positions of all permutations of the pattern in the text. In this paper,
Diptarama Hendrian +4 more
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String correction using the Damerau-Levenshtein distance
BMC Bioinformatics, 2019 Background In the string correction problem, we are to transform one string into another using a set of prescribed edit operations. In string correction using the Damerau-Levenshtein (DL) distance, the permissible edit operations are: substitution ...
Chunchun Zhao, Sartaj Sahni
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Toward Efficient Similarity Search under Edit Distance on Hybrid Architectures
Information, 2022 Edit distance is the most widely used method to quantify similarity between two strings. We investigate the problem of similarity search under edit distance.
Madiha Khalid +2 more
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Kendall tau sequence distance: Extending Kendall tau from ranks to sequences [PDF]
EAI Endorsed Transactions on Industrial Networks and Intelligent Systems, 2020 An edit distance is a measure of the minimum cost sequence of edit operations to transform one structureinto another. Edit distance can be used as a measure of similarity as part of a pattern recognition system, withlower values of edit distance implying
Vincent Cicirello
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An efficient rank based approach for closest string and closest substring. [PDF]
PLoS ONE, 2012 This paper aims to present a new genetic approach that uses rank distance for solving two known NP-hard problems, and to compare rank distance with other distance measures for strings.
Liviu P Dinu, Radu Ionescu
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