CINECA IRIS Institutional Research Information System
IRIS è la piattaforma adottata dall’Università degli Studi di Udine per gestire l’archivio aperto dei prodotti della ricerca. L’archivio contiene articoli, contributi in volume, monografie, interventi pubblicati in atti di convegno, Tesi di dottorato e altri materiali.
EnglishThe Burrows-Wheeler Transform is a text permutation that has revolutionized the fields of pattern matching and text compression, bridging the gap existing between the two. In this paper we approach the BWT-construction problem generalizing a well-known algorithm—based on backward search and dynamic strings manipulation—to work in a context-wise fashion, using automata on words. Let n , σ , and Hk be the text length, the alphabet size, and the k -th order empirical entropy of the text, respectively. Moreover, let H∗k=min{Hk+1,⌈logσ⌉} . Under the word RAM model with word size w∈Θ(logn) , our algorithm builds the BWT in average O(nH∗k) time using nH∗k+o(nH∗k) bits of space, where k=log_σ(n/log2n)−1 . We experimentally show that our algorithm has very good performances (essentially linear time) on DNA sequences, using about 2.6 bits per input symbol in RAM.
| Titolo: | Average Linear Time and Compressed Space Construction of the Burrows-Wheeler Transform | |
| Autori: | ||
| Data di pubblicazione: | 2015 | |
| Abstract: | The Burrows-Wheeler Transform is a text permutation that has revolutionized the fields of pattern matching and text compression, bridging the gap existing between the two. In this paper we approach the BWT-construction problem generalizing a well-known algorithm—based on backward search and dynamic strings manipulation—to work in a context-wise fashion, using automata on words. Let n , σ , and Hk be the text length, the alphabet size, and the k -th order empirical entropy of the text, respectively. Moreover, let H∗k=min{Hk+1,⌈logσ⌉} . Under the word RAM model with word size w∈Θ(logn) , our algorithm builds the BWT in average O(nH∗k) time using nH∗k+o(nH∗k) bits of space, where k=log_σ(n/log2n)−1 . We experimentally show that our algorithm has very good performances (essentially linear time) on DNA sequences, using about 2.6 bits per input symbol in RAM. | |
| Handle: | http://hdl.handle.net/11390/1063735 | |
| ISBN: | 978-3-319-15578-4 978-3-319-15579-1 978-3-319-15578-4 978-3-319-15579-1 | |
| Appare nelle tipologie: | 4.1 Contributo in Atti di convegno |
File in questo prodotto:
| File | Descrizione | Tipologia | Licenza | |
|---|---|---|---|---|
| lata2015.pdf | Articolo principale | Documento in Pre-print | Accesso ristretto Richiedi una copia |
Copyright © 2021