Results 21 to 30 of about 4,379 (204)
Compressed Spaced Suffix Arrays [PDF]
Mathematics in Computer Science, 2017 Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data structure, either a hash table or a spaced suffix array (SSA). In this paper we show how to compress SSAs relative
Travis Gagie +2 more
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Suffix Arrays in Parallel [PDF]
, 2003 Suffix arrays are powerful data structures for text indexing. In this paper we present parallel algorithms devised to increase throughput of suffix arrays on a multiple-query setting. Experimental results show that efficient performance is indeed feasible in this strongly sequential and very poor locality data structure.
Mauricio Marín, Gonzalo Navarro 0001
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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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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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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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CoRR, 2016 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 $(i)$ how we search for the right interval boundary impacts significantly the overall search speed, $(ii)$ a ...
Tomasz Marek Kowalski +3 more
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Costruzione space efficient di un suffix tree troncato con codifica TruST [PDF]
, 2022 Argomento della tesi è il suffix tree troncato, che ha la struttura ad albero ma occupa meno spazio del suffix tree. Il procedimento originariamente usato nella costruzione del suffix tree troncato con codifica TruST si basa sulla codifica derivata da ...
Pelizzari, Gabriele
core
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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Fast Lightweight Suffix Array Construction and Checking [PDF]
, 2003 We describe an algorithm that, for any $v\in[2,n]$, constructs the suffix array of a string of length $n$ in $\Oh{vn + n \log n}$ time using $\Oh{v+n/\sqrt{v}}$ space in addition to the input (the string) and the output (the suffix array). By setting $v=\
Juha Kärkkäinen +3 more
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RANCANG BANGUN APLIKASI PENCARIAN DOKUMEN BERBASIS WEB MENGGUNAKAN METODE SUFFIX CACTUS CLUSTERING
JUTI: Jurnal Ilmiah Teknologi Informasi, 2003 Salah satu bagian dari temu kembali (retrieval) informasi adalah menyajikan data hasil pencarian dengan cara mengelompokkan (clustering) seluruh dokumen hasil pencarian sesuai dengan kemiripan antar dokumen.
F. X. Arunanto, Agus Widodo
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