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pro vyhledávání: '"Goga, Adrián"'
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:
Baláz, Andrej, Gagie, Travis, Goga, Adrián, Heumos, Simon, Navarro, Gonzalo, Petescia, Alessia, Sirén, Jouni
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can preprocess a patt
Externí odkaz:
http://arxiv.org/abs/2308.09836
We give algorithms that, given a straight-line program (SLP) with $g$ rules that generates (only) a text $T [1..n]$, builds within $O(g)$ space the Lempel-Ziv (LZ) parse of $T$ (of $z$ phrases) in time $O(n\log^2 n)$ or in time $O(gz\log^2(n/z))$. We
Externí odkaz:
http://arxiv.org/abs/2212.02327
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the dataset. Unl
Externí odkaz:
http://arxiv.org/abs/2209.09218
Autor:
Goga, Adrián, Baláž, Andrej
We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from the same species. We combine two recent techniques from this area: Wheel
Externí odkaz:
http://arxiv.org/abs/2206.15097
Autor:
Budis, Jaroslav, Krampl, Werner, Kucharik, Marcel, Hekel, Rastislav, Goga, Adrian, Lichvar, Michal, Smolak, David, Bohmer, Miroslav, Balaz, Andrej, Duris, Frantisek, Gazdarica, Juraj, Soltys, Katarina, Turna, Jan, Radvanszky, Jan, Szemes, Tomas
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics p
Externí odkaz:
http://arxiv.org/abs/2106.13649
Autor:
Budiš Jaroslav, Krampl Werner, Kucharík Marcel, Hekel Rastislav, Goga Adrián, Sitarčík Jozef, Lichvár Michal, Smol’ak Dávid, Böhmer Miroslav, Baláž Andrej, Ďuriš František, Gazdarica Juraj, Šoltys Katarína, Turňa Ján, Radvánszky Ján, Szemes Tomáš
Publikováno v:
Journal of Integrative Bioinformatics, Vol 20, Iss 3, Pp 0021-6 (2023)
With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, w
Externí odkaz:
https://doaj.org/article/cdd1341e2cfa41c09c30b7750a7d7fcc
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.