Results 21 to 30 of about 37,020 (188)
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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Dynamic extended suffix arrays
Journal of Discrete Algorithms, 2010 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Salson, Mikael +3 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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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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Shortest Unique Substring Query Revisited [PDF]
, 2014 We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly improves the $O(
İleri, Atalay Mert +2 more
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CGAP-align: a high performance DNA short read alignment tool. [PDF]
PLoS ONE, 2013 Next generation sequencing platforms have greatly reduced sequencing costs, leading to the production of unprecedented amounts of sequence data. BWA is one of the most popular alignment tools due to its relatively high accuracy.
Yaoliang Chen +7 more
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Faster External Memory LCP Array Construction [PDF]
, 2016 The suffix array, perhaps the most important data structure in modern string processing, needs to be augmented with the longest-common-prefix (LCP) array in many applications. Their construction is often a major bottleneck especially when the data is too
, Kempa, Dominik
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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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IEEE Access, 2020 In order to achieve content-based binocular stereoscopic image or video retrieval efficiently, a feature indexing algorithm based on hybrid grid multiple suffix tree and hierarchical clustering is proposed.
Fengfeng Duan, Qicong Zhang
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