Results 21 to 30 of about 40,875 (196)
Fast Hybrid Data Structure for a Large Alphabet K-Mers Indexing for Whole Genome Alignment
IEEE Access, 2021 The most common index data structures used by whole genome aligners (WGA) are based on suffix trees (ST), suffix arrays, and FM-indexes. These data structures show good performance results as WGA works with sequences of letters over small alphabets; for ...
Rostislav Hrivnak +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 suitability of suffix arrays for lempel-ziv data compression [PDF]
, 2009 Lossless compression algorithms of the Lempel-Ziv (LZ) family are widely used nowadays. Regarding time and memory requirements, LZ encoding is much more demanding than decoding.
D. Gusfield +9 more
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Fully compressed suffix trees [PDF]
ACM Transactions on Algorithms, 2008 Suffix trees are by far the most important data structure in stringology, with a myriad of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require Θ( n log n ) bits of space, for a string of size n .
Luís M. S. Russo +2 more
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Subpath Queries on Compressed Graphs: A Survey
Algorithms, 2021 Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text T, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in T in time ...
Nicola Prezza
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Optimal Prefix and Suffix Queries on Texts [PDF]
Discrete Mathematics & Theoretical Computer Science, 2007 In this paper, we study a restricted version of the position restricted pattern matching problem introduced and studied by Mäkinen and Navarro [Position-Restricted Substring Searching, LATIN 2006].
Maxime Crochemore +2 more
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Reflexes of a Hurrian Word in Armenian: A Theonym, a Dendronym, an Anthroponym
Вопросы ономастики, 2021 In Old Armenian, saws means ‘proud, luxurious, great,’ ‘some (bright) color,’ and saws and sawsi mean ‘oriental plane tree’. The word has no etymology. Hurrian has the word šauša [sausa] ‘big, great’ and the theonym Šauša / Šauška for the local version ...
Armen Ye. Petrosyan
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The suffix binary search tree and suffix AVL tree
Journal of Discrete Algorithms, 2003 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Robert W. Irving, Lorna Love
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, 2017 The suffix tree—the compacted trie of all the suffixes of a string—is the most important and widely-used data structure in string processing. We consider a natural combinatorial question about suffix trees: for a string S of length n, how many nodes νS(d) can there be at (string) depth d in its suffix tree? We prove ν(n,d)=maxS∈ΣnνS(d) is O((n/d)logn) ,
Golnaz Badkobeh +3 more
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Cancer Informatics, 2009 Efficient and effective analysis of the growing genomic databases requires the development of adequate computational tools. We introduce a fast method based on the suffix tree data structure for predicting novel targets of hypoxia-inducible factor 1 (HIF-
Yue Jiang +6 more
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