Results 11 to 20 of about 4,379 (204)
RECONSTRUCTING A SUFFIX ARRAY [PDF]
International Journal of Foundations of Computer Science, 2006 For certain problems (for example, computing repetitions and repeats, data compression applications) it is not necessary that the suffixes of a string represented in a suffix tree or suffix array should occur in lexicographical order (lexorder). It thus becomes of interest to study possible alternate orderings of the suffixes in these data structures,
Franěk, F., Smyth, W.F.
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Dynamic extended suffix arrays [PDF]
Journal of Discrete Algorithms, 2010 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Salson, Mikael +3 more
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Scalable Parallel Suffix Array Construction [PDF]
Parallel Computing, 2006 Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. We describe the first implementation and experimental evaluation of a scalable parallel algorithm for suffix array construction.
Kulla, F., Sanders, P.
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Counting Suffix Arrays and Strings [PDF]
Theoretical Computer Science, 2005 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Schürmann, Klaus-Bernd, Stoye, Jens
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Fast index based algorithms and software for matching position specific scoring matrices [PDF]
BMC Bioinformatics, 2006 Background In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences.
Homann Robert +3 more
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Replacing suffix trees with enhanced suffix arrays [PDF]
Journal of Discrete Algorithms, 2004 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Mohamed Ibrahim Abouelhoda +2 more
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mkESA: enhanced suffix array construction tool. [PDF]
Bioinformatics, 2009 Homann R, Fleer D, Giegerich R, Rehmsmeier M. mkESA: enhanced suffix array construction tool. Bioinformatics. 2009;25(8):1084-1085.We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory
Homann R +3 more
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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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On the combinatorics of suffix arrays [PDF]
Information Processing Letters, 2013 We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of Burrows-Wheeler arrays given in [1], that we apply by reducing suffix sorting to cyclic shift sorting through the use of an ...
Kucherov, Gregory +2 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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