Results 11 to 20 of about 735,070 (175)
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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Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms, 2004 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Stefan Kurtz, Enno Ohlebusch
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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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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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A fast algorithm for constructing suffix arrays for DNA alphabets
Journal of King Saud University: Computer and Information Sciences, 2022 The continuous improvement of sequencing technologies has been paralleled by the development of efficient algorithms and data structures for sequencing data analysis and processing.
Zeinab Rabea +3 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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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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GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. [PDF]
PLoS ONE, 2014 DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity.
Shuji Suzuki +3 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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Computational and Structural Biotechnology Journal, 2022 Multiple DNA/RNA sequence alignment is an important fundamental tool in bioinformatics, especially for phylogenetic tree construction. With DNA-sequencing improvements, the amount of bioinformatics data is constantly increasing, and various tools need to
Ziyuan Wang +7 more
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