Generating Multiple Alignments of Genomes of the Same Species

Jannik Olbrich, Thomas Büchler, Enno Ohlebusch

2025

Abstract

In this paper, we tackle the problem of generating a multiple alignment of assembled genomes of individuals of the same species. Of course, a (colinear) multiple alignment cannot capture structural variants such as inversions or transpositions, but if these are relatively rare (as, for instance, in human or mouse genomes), it makes sense to generate such a multiple alignment. In the following, it is assumed that each assembled genome is composed of contigs. We will show that the combination of a well-known anchor-based method with the technique of prefix-free parsing yields an approach that is able to generate multiple alignments on a pangenomic scale, provided that large structural variants are rare. Furthermore, experiments with real world data show that our software tool PANAMA (PANgenomic Anchor-based Multiple Alignment) significantly outperforms current state-of-the art programs.

Paper Citation

in Harvard Style

Olbrich J., Büchler T. and Ohlebusch E. (2025). Generating Multiple Alignments of Genomes of the Same Species. In Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS; ISBN 978-989-758-731-3, SciTePress, pages 459-468. DOI: 10.5220/0013165400003911

in Bibtex Style

@conference{bioinformatics25,
author={Jannik Olbrich and Thomas Büchler and Enno Ohlebusch},
title={Generating Multiple Alignments of Genomes of the Same Species},
booktitle={Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS},
year={2025},
pages={459-468},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0013165400003911},
isbn={978-989-758-731-3},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS
TI - Generating Multiple Alignments of Genomes of the Same Species
SN - 978-989-758-731-3
AU - Olbrich J.
AU - Büchler T.
AU - Ohlebusch E.
PY - 2025
SP - 459
EP - 468
DO - 10.5220/0013165400003911
PB - SciTePress