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Documents authored by Guerrini, Veronica

Document
DOI: 10.4230/LIPIcs.CPM.2024.7
A Class of Heuristics for Reducing the Number of BWT-Runs in the String Ordering Problem

Authors: Gianmarco Bertola, Anthony J. Cox, Veronica Guerrini, and Giovanna Rosone

Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)

Abstract
The Burrows-Wheeler transform (BWT) is a famous text transformation that rearranges the symbols of the input strings so that occurrences of a same symbol tend to occur in runs. The number of runs is an important parameter in the BWT output string, historically associated with its high compressibility and more recently used as a measure for the space complexity of efficient data structures. It is a known fact that reordering the strings in the input collection 𝒮 affects the number of runs in the output string bwt(𝒮) produced by applying the BWT to the string collection. In this paper, we define a class of transformed strings where symbols in particular blocks of the bwt(𝒮) can be reordered according to a different adaptive alphabet order. Then, we introduce new heuristics to reduce the number of runs in the BWT output of a string collection that improve on the two existing heuristics introduced in Cox et al. [Anthony J. Cox et al., 2012]. These new heuristics are computed when applying the BWT to a string collection assuming no a priori order on the input strings and without requiring any pre- and/or post- processing of the collection 𝒮 or of the BWT string. In this paper, we also face the problem of reconstructing the input collection 𝒮 from the string bwt(𝒮) together with the string permutation realized when applying an alphabetical reordering of symbols during the construction of bwt(𝒮).
Cite as

Gianmarco Bertola, Anthony J. Cox, Veronica Guerrini, and Giovanna Rosone. A Class of Heuristics for Reducing the Number of BWT-Runs in the String Ordering Problem. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 7:1-7:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bertola_et_al:LIPIcs.CPM.2024.7,
  author =	{Bertola, Gianmarco and Cox, Anthony J. and Guerrini, Veronica and Rosone, Giovanna},
  title =	{{A Class of Heuristics for Reducing the Number of BWT-Runs in the String Ordering Problem}},
  booktitle =	{35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)},
  pages =	{7:1--7:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-326-3},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{296},
  editor =	{Inenaga, Shunsuke and Puglisi, Simon J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.7},
  URN =		{urn:nbn:de:0030-drops-201179},
  doi =		{10.4230/LIPIcs.CPM.2024.7},
  annote =	{Keywords: Burrows-Wheeler Transform, SAP-interval, repetitive text, string compression}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.23
phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering

Authors: Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone, and Lorenzo Tattini

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
Molecular phylogenetics is a fundamental branch of biology. It studies the evolutionary relationships among the individuals of a population through their biological sequences, and may provide insights about the origin and the evolution of viral diseases, or highlight complex evolutionary trajectories. In this paper we develop a method called phyBWT, describing how to use the extended Burrows-Wheeler Transform (eBWT) for a collection of DNA sequences to directly reconstruct phylogeny, bypassing the alignment against a reference genome or de novo assembly. Our phyBWT hinges on the combinatorial properties of the eBWT positional clustering framework. We employ eBWT to detect relevant blocks of the longest shared substrings of varying length (unlike the k-mer-based approaches that need to fix the length k a priori), and build a suitable decomposition leading to a phylogenetic tree, step by step. As a result, phyBWT is a new alignment-, assembly-, and reference-free method that builds a partition tree without relying on the pairwise comparison of sequences, thus avoiding to use a distance matrix to infer phylogeny. The preliminary experimental results on sequencing data show that our method can handle datasets of different types (short reads, contigs, or entire genomes), producing trees of quality comparable to that found in the benchmark phylogeny.
Cite as

Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone, and Lorenzo Tattini. phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 23:1-23:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{guerrini_et_al:LIPIcs.WABI.2022.23,
  author =	{Guerrini, Veronica and Conte, Alessio and Grossi, Roberto and Liti, Gianni and Rosone, Giovanna and Tattini, Lorenzo},
  title =	{{phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{23:1--23:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.23},
  URN =		{urn:nbn:de:0030-drops-170577},
  doi =		{10.4230/LIPIcs.WABI.2022.23},
  annote =	{Keywords: Phylogeny, partition tree, BWT, positional cluster, alignment-free, reference-free, assembly-free}
}
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