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Updated: May 21, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
Generating multiple alignments on a pangenomic scale
Jannik Olbrich1, Thomas Büchler1, Enno Ohlebusch1
1Institute of Theoretical Computer Science, Ulm University, Ulm, 89069, Germany.
Motivation:
Since novel long read sequencing technologies allow for de novo assembly of many individuals of a species, high-quality assemblies are becoming widely available. For example, the recently published draft human pangenome reference was based on assemblies composed of contigs. There is an urgent need for a software-tool that is able to generate a multiple alignment of genomes of the same species because current multiple sequence alignment programs cannot deal with such a volume of data.
Results:
We 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-scale structural variants are rare. Furthermore, experiments with real world data show that our software tool PANgenomic Anchor-based Multiple Alignment significantly outperforms current state-of-the art programs.
Availability And Implementation:
Source code is available at: https://gitlab.com/qwerzuiop/panama, archived at swh:1:dir:e90c9f664995acca9063245cabdd97549cf39694.
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