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pro vyhledávání: '"Brown, Nathaniel K."'
We consider how to reorder the rows of Nishimoto and Tabei's move structure such that we more often move from one row to the next in memory.
Externí odkaz:
http://arxiv.org/abs/2407.18956
Autor:
Goga, Adrián, Depuydt, Lore, Brown, Nathaniel K., Fostier, Jan, Gagie, Travis, Navarro, Gonzalo
MONI (Rossi et al., {\it JCB} 2022) is a BWT-based compressed index for computing the matching statistics and maximal exact matches (MEMs) of a pattern (usually a DNA read) with respect to a highly repetitive text (usually a database of genomes) usin
Externí odkaz:
http://arxiv.org/abs/2311.04538
Autor:
Martínez-Guardiola, César, Brown, Nathaniel K., Silva-Coira, Fernando, Köppl, Dominik, Gagie, Travis, Ladra, Susana
MONI (Rossi et al., 2022) can store a pangenomic dataset T in small space and later, given a pattern P, quickly find the maximal exact matches (MEMs) of P with respect to T. In this paper we consider its one-pass version (Boucher et al., 2021), whose
Externí odkaz:
http://arxiv.org/abs/2211.07794
Publikováno v:
20th International Symposium on Experimental Algorithms (2022), volume 233, pages 16:1--16:16
Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit lower bound
Externí odkaz:
http://arxiv.org/abs/2112.04271
Autor:
Martínez-Guardiola, César, Brown, Nathaniel K., Silva-Coira, Fernando, Köppl, Dominik, Gagie, Travis, Ladra, Susana
Publikováno v:
2023 Data Compression Conference (DCC).
MONI (Rossi et al., 2022) can store a pangenomic dataset T in small space and later, given a pattern P, quickly find the maximal exact matches (MEMs) of P with respect to T. In this paper we consider its one-pass version (Boucher et al., 2021), whose
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3c24da284e423180234a73fec69eaa71
https://doi.org/10.1109/dcc55655.2023.00035
https://doi.org/10.1109/dcc55655.2023.00035
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Nov 02. Date of Electronic Publication: 2024 Nov 02.
Autor:
Hwang S; XDBio Program, Johns Hopkins University, Baltimore MD, USA., Brown NK; Department of Computer Science, Johns Hopkins University, Baltimore MD, USA., Ahmed OY; Department of Computer Science, Johns Hopkins University, Baltimore MD, USA., Jenike KM; Department of Computer Science, Johns Hopkins University, Baltimore MD, USA., Kovaka S; Department of Computer Science, Johns Hopkins University, Baltimore MD, USA., Schatz MC; Department of Computer Science, Johns Hopkins University, Baltimore MD, USA., Langmead B; Department of Computer Science, Johns Hopkins University, Baltimore MD, USA.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 May 22. Date of Electronic Publication: 2024 May 22.
Autor:
Goga A; Dept. of Comp. Sci., Comenius University, Bratislava, Slovakia., Depuydt L; Dept. of Inf. Tech., Ghent University, Ghent, Belgium., Brown NK; Dept. of Comp. Sci., Johns Hopkins University, Baltimore, USA., Fostier J; Dept. of Inf. Tech., Ghent University, Ghent, Belgium., Gagie T; CeBiB & Fac. of Comp. Sci., Dalhousie University, Halifax, Canada., Navarro G; CeBiB & Dept. of Comp. Sci., University of Chile, Santiago, Chile.
Publikováno v:
Proceedings. Data Compression Conference [Proc Data Compress Conf] 2024 Mar; Vol. 2024, pp. 123-132. Date of Electronic Publication: 2024 May 21.
Autor:
Zakeri M; Department of Computer Science, Johns Hopkins University., Brown NK; Department of Computer Science, Johns Hopkins University., Ahmed OY; Department of Computer Science, Johns Hopkins University., Gagie T; Faculty of Computer Science, Dalhousie University., Langmead B; Department of Computer Science, Johns Hopkins University.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Feb 15. Date of Electronic Publication: 2024 Feb 15.
Autor:
Martínez-Guardiola C; Universidade da Coruña, CITIC, A Coruña, Spain., Brown NK; Dalhousie U, Halifax, Canada., Silva-Coira F; Universidade da Coruña, CITIC, A Coruña, Spain., Köppl D; TMDU, Tokyo, Japan., Gagie T; Dalhousie U, Halifax, Canada., Ladra S; Universidade da Coruña, CITIC, A Coruña, Spain.
Publikováno v:
Proceedings. Data Compression Conference [Proc Data Compress Conf] 2023 Mar; Vol. 2023, pp. 268-277. Date of Electronic Publication: 2023 May 19.