Results 21 to 30 of about 735,070 (175)
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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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 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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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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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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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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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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Massively parallel suffix array construction
, 1998 This paper considers the construction of the suffix array of a string on the MasPar MP-2 architecture. Suffix arrays are space-efficient variants of the suffix trees, a fundamental dictionary data structure that is the backbone of many string algorithms ...
Rovan, B, Korda, M
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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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