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pro vyhledávání: '"Suffix array"'
We present first algorithmic ideas for a practical and lightweight adaption of the DCX suffix array construction algorithm [Sanders et al., 2003] to the distributed-memory setting. Our approach relies on a bucketing technique which enables a lightwei
Externí odkaz:
http://arxiv.org/abs/2412.10160
Akademický článek
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Autor:
Nishimoto, Takaaki, Tabei, Yasuo
Big data, encompassing extensive datasets, has seen rapid expansion, notably with a considerable portion being textual data, including strings and texts. Simple compression methods and standard data structures prove inadequate for processing these da
Externí odkaz:
http://arxiv.org/abs/2404.07510
Autor:
Lecroq, Thierry
String matching is the problem of finding all the occurrences of a pattern in a text. It has been intensively studied and the Boyer-Moore string matching algorithm is probably one of the most famous solution to this problem. This algorithm uses two p
Externí odkaz:
http://arxiv.org/abs/2402.16469
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-16 (2024)
Abstract Purpose String indexes such as the suffix array (sa) and the closely related longest common prefix (lcp) array are fundamental objects in bioinformatics and have a wide variety of applications. Despite their importance in practice, few scala
Externí odkaz:
https://doaj.org/article/79aae57e7f2345199d9e1c1cff770744
Autor:
Baláž, Andrej, Petescia, Alessia
A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and read mapping.
Externí odkaz:
http://arxiv.org/abs/2306.14689
Publikováno v:
Intelligent Data Analysis. 2021, Vol. 25 Issue 2, p283-303. 21p.
Akademický článek
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The suffix array is arguably one of the most important data structures in sequence analysis and consequently there is a multitude of suffix sorting algorithms. However, to this date the GSACA algorithm introduced in 2015 is the only known non-recursi
Externí odkaz:
http://arxiv.org/abs/2206.12222
Autor:
Kempa, Dominik, Kociumaka, Tomasz
The suffix array $SA[1..n]$ of a text $T$ of length $n$ is a permutation of $\{1,\ldots,n\}$ describing the lexicographical ordering of suffixes of $T$, and it is considered to be among of the most important data structures in string algorithms, with
Externí odkaz:
http://arxiv.org/abs/2201.01285