License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.ISAAC.2021.40
URN: urn:nbn:de:0030-drops-154734
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2021/15473/
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Araujo, Eloi ; Rozante, Luiz C. ; Rubert, Diego P. ; Martinez, Fábio V.

Algorithms for Normalized Multiple Sequence Alignments

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LIPIcs-ISAAC-2021-40.pdf (1.0 MB)

Abstract

Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and other fields. While the alignment of two sequences may be performed swiftly in many applications, the simultaneous alignment of multiple sequences proved to be naturally more intricate. Although most multiple sequence alignment (MSA) formulations are NP-hard, several approaches have been developed, as they can outperform pairwise alignment methods or are necessary for some applications. Taking into account not only similarities but also the lengths of the compared sequences (i.e. normalization) can provide better alignment results than both unnormalized or post-normalized approaches. While some normalized methods have been developed for pairwise sequence alignment, none have been proposed for MSA. This work is a first effort towards the development of normalized methods for MSA. We discuss multiple aspects of normalized multiple sequence alignment (NMSA). We define three new criteria for computing normalized scores when aligning multiple sequences, showing the NP-hardness and exact algorithms for solving the NMSA using those criteria. In addition, we provide approximation algorithms for MSA and NMSA for some classes of scoring matrices.

BibTeX - Entry

@InProceedings{araujo_et_al:LIPIcs.ISAAC.2021.40,
  author =	{Araujo, Eloi and Rozante, Luiz C. and Rubert, Diego P. and Martinez, F\'{a}bio V.},
  title =	{{Algorithms for Normalized Multiple Sequence Alignments}},
  booktitle =	{32nd International Symposium on Algorithms and Computation (ISAAC 2021)},
  pages =	{40:1--40:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-214-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{212},
  editor =	{Ahn, Hee-Kap and Sadakane, Kunihiko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/15473},
  URN =		{urn:nbn:de:0030-drops-154734},
  doi =		{10.4230/LIPIcs.ISAAC.2021.40},
  annote =	{Keywords: Multiple sequence alignment, Normalized multiple sequence alignment, Algorithms and complexity}
}

Keywords: Multiple sequence alignment, Normalized multiple sequence alignment, Algorithms and complexity
Collection: 32nd International Symposium on Algorithms and Computation (ISAAC 2021)
Issue Date: 2021
Date of publication: 30.11.2021

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