Results 31 to 40 of about 4,379 (204)
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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Sampling the Suffix Array with Minimizers [PDF]
, 2015 Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches compared to the sparse suffix array, for long enough patterns.
Szymon Grabowski, Marcin Raniszewski
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Analisi sperimentale delle prestazioni di un suffix tree troncato [PDF]
, 2022 Le strutture dati sono un ambito di ricerca estremamente vivo, poiché adatte a risolvere un ampio numero di problemi d'indicizzazione. Tra le varie strutture dati, particolare rilevanza hanno le strutture dati basate sui suffissi, che si prestano ...
Zucchetto, Daniel
core
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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Linear-time Suffix Sorting - A New Approach for Suffix Array Construction [PDF]
, 2016 This paper presents a new approach for linear-time suffix sorting. It introduces a new sorting principle that can be used to build the first non-recursive linear-time suffix array construction algorithm named GSACA. Although GSACA cannot keep up with the
Baier, Uwe
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Pengkontruksian Bidirected Overlap Graph untuk Perakitan Sekuens DNA
Jurnal Teknologi Informasi dan Ilmu Komputer, 2020 De novo DNA (Deoxyribonucleic Acid) sequence assembly atau perakitan sekuens DNA secara De novo adalah tahapan yang sangat penting dalam analisis sekuens DNA.
Wisnu Ananta Kusuma, Albert Adrianus
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BMC Bioinformatics, 2023 Background A large number of researchers have devoted to accelerating the speed of genome sequencing and reducing the cost of genome sequencing for decades, and they have made great strides in both areas, making it easier for researchers to study and ...
Zhiwen Lu +3 more
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Human Language Technologies 2007: The Conference of the North American Chapter of the Association for Computational Linguistics; Companion Volume, Short Papers on XX - NAACL '07, 2007 Suppose we have a large dictionary of strings. Each entry starts with a figure of merit (popularity). We wish to find the k-best matches for a substring, s, in a dictinoary, dict. That is, grep s dict | sort -n | head -k, but we would like to do this in sublinear time.
Kenneth Ward Church +2 more
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Algorithms for enhanced suffix array [PDF]
, 2009 Suffix tree is one of the most important data structures in string processing. However, the space consumption of the suffix tree is a bottleneck in large scale applications. Suffix array is by contrast a space efficient data structure having not so large
Šedek, Jindřich
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An optimized FM-index library for nucleotide and amino acid search
Algorithms for Molecular Biology, 2021 Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text ...
Tim Anderson, Travis J. Wheeler
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