Results 11 to 20 of about 37,020 (188)
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.
Abouelhoda, Mohamed Ibrahim +2 more
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Better external memory suffix array construction
ACM Journal of Experimental Algorithmics, 2008 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. However, so far, it has appeared prohibitive to build suffix arrays for huge inputs that do not fit into main memory. This paper presents design,
Dementiev, Roman +3 more
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Faster run-length compressed suffix arrays [PDF]
Oasics : openaccess series in informaticsWe first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $σ$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n / r) + r \log σ+ σ\right)$ bits such that later, given character $a$ and the suffix array interval for $P$, we can find ...
Brown N. K. +4 more
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Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets [PDF]
BMC BioinformaticsIdentification of microorganisms in a biological sample is a crucial step in diagnostics, pathogen screening, biomedical research, evolutionary studies, agriculture, and biological threat assessment.
Burak Demiralay, Tolga Can
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A bioinformatician's guide to the forefront of suffix array construction algorithms. [PDF]
Brief Bioinform, 2014 Shrestha AM, Frith MC, Horton P.
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Generic Non-recursive Suffix Array Construction
ACM Transactions on AlgorithmsThe suffix array is arguably one of the most important data structures in sequence analysis and consequently there is a multitude of suffix sorting algorithms. However, to this date the GSACA algorithm introduced in 2015 is the only known non-recursive linear-time suffix array construction algorithm (SACA).
Jannik Olbrich +2 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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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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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
González, Rodrigo +2 more
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