Results 11 to 20 of about 37,210 (201)
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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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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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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Locally Compressed Suffix Arrays [PDF]
ACM Journal of Experimental Algorithmics, 2015 We introduce a compression technique for suffix arrays. It is sensitive to the compressibility of the text and local , meaning that random portions of the suffix array can be decompressed by accessing mostly contiguous memory areas. This makes decompression very fast, especially when various contiguous cells must be
Rodrigo González +2 more
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Suffix-Sorting via Shannon-Fano-Elias Codes
Algorithms, 2010 Given a sequence T = t0t1 . . . tn-1 of size n = |T|, with symbols from a fixed alphabet Σ, (|Σ| ≤ n), the suffix array provides a listing of all the suffixes of T in a lexicographic order.
Donald Adjeroh, Fei Nan
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On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching [PDF]
, 2016 We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$
Fischer, Johannes +2 more
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Computing and Informatics, 2019 The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show that i) the way how we search for the right interval boundary impacts significantly the overall search speed, ii ...
Kowalski, Tomasz M. +2 more
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GeDi: applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes
BMC Bioinformatics, 2020 Background Current popular variant calling pipelines rely on the mapping coordinates of each input read to a reference genome in order to detect variants.
Izaak Coleman +5 more
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