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About 742 papers for “Suffix array”
Langmead, Benjamin · Figshare · 2024
I discuss how to build a suffix tree, starting with a sorting algorithm. Then I discuss construction via the suffix tree. I finish by pointing to some more modern algorithms for direct construction of the suffix array.
Cited by 0Open access
Langmead, Benjamin · Figshare · 2024
I discuss how to build a suffix tree, starting with a sorting algorithm. Then I discuss construction via the suffix tree. I finish by pointing to some more modern algorithms for direct construction of the suffix array.
Cited by 0Open access
Juha Kärkkäinen · Encyclopedia of Algorithms · 2008
Cited by 0
Djamal Belazzougui, Veli Mäkinen, Daniel Valenzuela · Encyclopedia of Algorithms · 2016
Cited by 1
Antea Hadviger · FER Repository · 2015
U bioinformatici često se javlja problem pretraživanja veoma dugačkih nizova (DNA sljedova) s različitim uzorcima pretrage. Kako bi se problem riješio u razumnom vremenu, potrebno je koristiti efikasne strukture indeksiranja teksta, kao što su sufiksno stablo i poboljšano sufiksno polje. Poboljšano sufiksno polje sastoji se od običnog sufiksnog polja i dodatnih struktura (polje najduljih zajedničkih prefiksa, tablica djece). Uz manje memorijsko zauzeće, jednostavniju implementaciju i linearno vrijeme izgradnje, koristeći algoritme kao što je SA-IS, u praksi nadmašuje sufiksno stablo zadržavajući svu kompleksnu funkcionalnost.
Cited by 0
Djamal Belazzougui, VeliMä kinen, Daniel Valenzuela · Encyclopedia of Algorithms · 2014
Cited by 2
Juha Kärkkäinen · Encyclopedia of Algorithms · 2016
Cited by 5
Langmead, Benjamin · Figshare · 2024
I show how combining information about Longest Common Prefixes (LCP) as well as pre-computed information about Longest Common Extensions (LCE) allows us to achieve a O(n + log m) algorithm for querying the suffix array.
Cited by 0Open access
Langmead, Benjamin · Figshare · 2024
I show how combining information about Longest Common Prefixes (LCP) as well as pre-computed information about Longest Common Extensions (LCE) allows us to achieve a O(n + log m) algorithm for querying the suffix array.
Cited by 0Open access
Langmead, Benjamin · Figshare · 2024
Here I discuss basic algorithms for querying the suffix tree along with their time complexities. These include queries that check for presence or absence of substrings, queries the count the number of times a substring occurs, and queries that report all offsets where a substring occurs.
Cited by 0Open access
Langmead, Benjamin · Figshare · 2024
Here I discuss basic algorithms for querying the suffix tree along with their time complexities. These include queries that check for presence or absence of substrings, queries the count the number of times a substring occurs, and queries that report all offsets where a substring occurs.
Cited by 0Open access
M. Leonard, Laurent Mouchard, M. Salson · HAL (Le Centre pour la Communication Scientifique Directe) · 2009
International audience
Cited by 0
Mikaël Salson, Thierry Lecroq, Martine Léonard et al. · HAL (Le Centre pour la Communication Scientifique Directe) · 2010
Cited by 0
Laurent Mouchard, Hal Id Inria, L. Mouchard et al. · 2011
Cited by 0
František Franěk, William F. Smyth · International Journal of Foundations of Computer Science · 2006
For certain problems (for example, computing repetitions and repeats, data compression applications) it is not necessary that the suffixes of a string represented in a suffix tree or suffix array should occur in lexicographical order (lexorder). It thus becomes of interest to study possible alternate orderings of the suffixes in these data structures, that may be easier to construct or more efficient to use. In this paper we consider the "reconstruction" of a suffix array based on a given reordering of the alphabet, and we describe simple time- and space-efficient algorithms that accomplish it.
Cited by 9
Miroslav Balík · Lecture notes in computer science · 2003
Cited by 3
Pavel Žoha · Digital Repository (National Repository of Grey Literature) · 2007
Suffix array is a data structure used for string operations such as pattern matching. It is also useful for some lossless data compression algorithms. In this paper I present a comparison of several di erent ways to construct it (algorithms of Manber & Myers, Kárkkáinen & Sanders, Seward, Manzini & Ferragina and Ukkonen's algorithm for suffix tree construction). I implemented these methodes and together with common sorting algorithms (mergesort, quicksort, heapsort and shellsort) tested both on standard data les and on randomly generated les of di erent alphabet sizes. I also studied the possibility of using these algorithms for inputs of alphabet greater than 256 characters.
Cited by 0
Langmead, Benjamin · Figshare · 2024
I define the idea of the Longest Common Prefix (LCP) and discuss how keeping track of LCPs observed earlier in the search process enables us to skip character comparisons later in the search process.
Cited by 0Open access
Langmead, Benjamin · Figshare · 2024
I define the idea of the Longest Common Prefix (LCP) and discuss how keeping track of LCPs observed earlier in the search process enables us to skip character comparisons later in the search process.
Cited by 0Open access
Michael A. Maniscalco, et al. · 2011
The suffix array is a data structure formed by sorting the suffixes of a string into lexicographical order. It is important for a variety of applications, perhaps most notably pattern matching, pattern discovery and block-sorting data compression. The last decade has seen intensive research toward efficient construction of suffix arrays with algorithms striving not only to be fast, but also “lightweight” (in the sense that they use small working memory). In this paper we describe a new lightweight suffix array construction algorithm. By exploiting several interesting properties of suffixes in combination with cache concious programming we acheive excellent runtimes. Extensive experiments show our approach to be faster that all other known algorithms for the task.
Cited by 0