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Documents authored by Holub, Jan

Document
DOI: 10.4230/LIPIcs.SEA.2024.10
Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests

Authors: Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, and Gonzalo Navarro

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular classifiers such as Kraken use k-mers, recent research indicates that using maximal exact matches (MEMs) can lead to better classifications. For example, we can - build an augmented FM-index over the the genomes in the tree concatenated in left-to-right order; - for each MEM in a read, find the interval in the suffix array containing the starting positions of that MEM’s occurrences in those genomes; - find the minimum and maximum values stored in that interval; - take the lowest common ancestor (LCA) of the genomes containing the characters at those positions. This solution is practical, however, only when the total size of the genomes in the tree is fairly small. In this paper we consider applying the same solution to three lossily compressed representations of the genomes' concatenation: - a KATKA kernel, which discards characters that are not in the first or last occurrence of any k_max-tuple, for a parameter k_max; - a minimizer digest; - a KATKA kernel of a minimizer digest. With a test dataset and these three representations of it, simulated reads and various parameter settings, we checked how many reads' longest MEMs occurred only in the sequences from which those reads were generated ("true positive" reads). For some parameter settings we achieved significant compression while only slightly decreasing the true-positive rate.
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Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, and Gonzalo Navarro. Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{draesslerova_et_al:LIPIcs.SEA.2024.10,
  author =	{Draesslerov\'{a}, Dominika and Ahmed, Omar and Gagie, Travis and Holub, Jan and Langmead, Ben and Manzini, Giovanni and Navarro, Gonzalo},
  title =	{{Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{10:1--10:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.10},
  URN =		{urn:nbn:de:0030-drops-203756},
  doi =		{10.4230/LIPIcs.SEA.2024.10},
  annote =	{Keywords: Taxonomic classification, metagenomics, KATKA, maximal exact matches, string kernels, minimizer digests}
}
Document
Complete Volume
DOI: 10.4230/LIPIcs.CPM.2022
LIPIcs, Volume 223, CPM 2022, Complete Volume

Authors: Hideo Bannai and Jan Holub

Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

Abstract
LIPIcs, Volume 223, CPM 2022, Complete Volume
Cite as

33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 1-470, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@Proceedings{bannai_et_al:LIPIcs.CPM.2022,
  title =	{{LIPIcs, Volume 223, CPM 2022, Complete Volume}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{1--470},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-234-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{223},
  editor =	{Bannai, Hideo and Holub, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022},
  URN =		{urn:nbn:de:0030-drops-161265},
  doi =		{10.4230/LIPIcs.CPM.2022},
  annote =	{Keywords: LIPIcs, Volume 223, CPM 2022, Complete Volume}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.CPM.2022.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Hideo Bannai and Jan Holub

Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
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33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 0:i-0:xviii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bannai_et_al:LIPIcs.CPM.2022.0,
  author =	{Bannai, Hideo and Holub, Jan},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{0:i--0:xviii},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-234-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{223},
  editor =	{Bannai, Hideo and Holub, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.0},
  URN =		{urn:nbn:de:0030-drops-161271},
  doi =		{10.4230/LIPIcs.CPM.2022.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.20
Byte-Aligned Pattern Matching in Encoded Genomic Sequences

Authors: Petr Procházka and Jan Holub

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
In this article, we propose a novel pattern matching algorithm, called BAPM, that performs searching in the encoded genomic sequences. The algorithm works at the level of single bytes and it achieves sublinear performance on average. The preprocessing phase of the algorithm is linear with respect to the size of the searched pattern m. A simple O(m)-space data structure is used to store all factors (with a defined length) of the searched pattern. These factors are later searched during the searching phase which ensures sublinear time on average. Our algorithm significantly overcomes the state-of-the-art pattern matching algorithms in the locate time on middle and long patterns. Furthermore, it is able to cooperate very easily with the block q-gram inverted index. The block q-gram inverted index together with our pattern matching algorithm achieve superior results in terms of locate time to the current index data structures for less frequent patterns. We present experimental results using real genomic data. These results prove efficiency of our algorithm.
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Petr Procházka and Jan Holub. Byte-Aligned Pattern Matching in Encoded Genomic Sequences. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 20:1-20:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{prochazka_et_al:LIPIcs.WABI.2017.20,
  author =	{Proch\'{a}zka, Petr and Holub, Jan},
  title =	{{Byte-Aligned Pattern Matching in Encoded Genomic Sequences}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{20:1--20:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.20},
  URN =		{urn:nbn:de:0030-drops-76538},
  doi =		{10.4230/LIPIcs.WABI.2017.20},
  annote =	{Keywords: genomic sequences, pattern matching, q-gram inverted index}
}
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