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DOI: 10.4230/LIPIcs.CPM.2026.29

The TAG Array of a Multiple Sequence Alignment

Authors: Jannik Olbrich and Enno Ohlebusch

Published in: LIPIcs, Volume 369, 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)

Abstract

Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs, this has the advantage that efficient exact search via indexes based on the Burrows-Wheeler Transform (BWT) is possible, that no chimeric sequences are created, and that the results are not influenced by heuristics. However, such an index may report a match in thousands of positions even if these all correspond to the same locus, making downstream analysis unnecessarily more expensive. For sufficiently similar sequences (e.g. human chromosomes), a multiple sequence alignment (MSA) can be computed. Since an MSA tends to group similar strings in the same columns, it is likely that a string occurring thousands of times in the pangenome can be described by very few columns in the MSA. We describe a method to tag entries in the BWT with the corresponding column in the MSA and develop an index that can map matches in the BWT to columns in the MSA in time proportional to the output. As a by-product, we can project a match to a designated reference genome, a capability that current pangenome aligners lack.

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Jannik Olbrich and Enno Ohlebusch. The TAG Array of a Multiple Sequence Alignment. In 37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 369, pp. 29:1-29:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{olbrich_et_al:LIPIcs.CPM.2026.29,
  author =	{Olbrich, Jannik and Ohlebusch, Enno},
  title =	{{The TAG Array of a Multiple Sequence Alignment}},
  booktitle =	{37th Annual Symposium on Combinatorial Pattern Matching (CPM 2026)},
  pages =	{29:1--29:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-420-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{369},
  editor =	{Bille, Philip and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.29},
  URN =		{urn:nbn:de:0030-drops-259555},
  doi =		{10.4230/LIPIcs.CPM.2026.29},
  annote =	{Keywords: Burrows-Wheeler Transform, pattern matching, index data structure, pangenomics}
}

Document

DOI: 10.4230/OASIcs.Manzini.8

A Taxonomy of LCP-Array Construction Algorithms

Authors: Johannes Fischer and Enno Ohlebusch

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract

The combination of the suffix array and the LCP-array can be used to solve many string processing problems efficiently. We review some of the most important sequential LCP-array construction algorithms in random access memory.

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Johannes Fischer and Enno Ohlebusch. A Taxonomy of LCP-Array Construction Algorithms. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 8:1-8:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fischer_et_al:OASIcs.Manzini.8,
  author =	{Fischer, Johannes and Ohlebusch, Enno},
  title =	{{A Taxonomy of LCP-Array Construction Algorithms}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{8:1--8:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.8},
  URN =		{urn:nbn:de:0030-drops-239166},
  doi =		{10.4230/OASIcs.Manzini.8},
  annote =	{Keywords: longest common prefix array, suffix array, Burrows-Wheeler transform}
}

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Documents authored by Ohlebusch, Enno

The TAG Array of a Multiple Sequence Alignment

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A Taxonomy of LCP-Array Construction Algorithms

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