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DOI: 10.4230/LIPIcs.WABI.2024.21

McDag: Indexing Maximal Common Subsequences in Practice

Authors: Giovanni Buzzega, Alessio Conte, Roberto Grossi, and Giulia Punzi

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract

Analyzing and comparing sequences of symbols is among the most fundamental problems in computer science, possibly even more so in bioinformatics. Maximal Common Subsequences (MCSs), i.e., inclusion-maximal sequences of non-contiguous symbols common to two or more strings, have only recently received attention in this area, despite being a basic notion and a natural generalization of more common tools like Longest Common Substrings/Subsequences. In this paper we simplify and engineer recent advancements on MCSs into a practical tool called McDag, the first publicly available tool that can index MCSs of real genomic data. We demonstrate that our tool can index sequences exceeding 10,000 base pairs within minutes, utilizing only 4-7% more than the minimum required nodes, while also extracting relevant insights.

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Giovanni Buzzega, Alessio Conte, Roberto Grossi, and Giulia Punzi. McDag: Indexing Maximal Common Subsequences in Practice. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 21:1-21:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{buzzega_et_al:LIPIcs.WABI.2024.21,
  author =	{Buzzega, Giovanni and Conte, Alessio and Grossi, Roberto and Punzi, Giulia},
  title =	{{McDag: Indexing Maximal Common Subsequences in Practice}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{21:1--21:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.21},
  URN =		{urn:nbn:de:0030-drops-206650},
  doi =		{10.4230/LIPIcs.WABI.2024.21},
  annote =	{Keywords: Index data structure, DAG, Common subsequence, Inclusion-wise maximality, LCS}
}

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McDag: Indexing Maximal Common Subsequences in Practice

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