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TECHNOLOGY AND CODE article

Front. Bioinform.
Sec. Network Bioinformatics
Volume 4 - 2024 | doi: 10.3389/fbinf.2024.1358374
This article is part of the Research Topic Networks and Graphs in Biological Data: Current Methods, Opportunities and Challenges View all 3 articles

A Layout Framework for genome-wide Multiple Sequence Alignment Graphs

Provisionally accepted
Jeremias Schebera Jeremias Schebera 1,2*Dirk Zeckzer Dirk Zeckzer 1Daniel Wiegreffe Daniel Wiegreffe 1
  • 1 Leipzig University, Leipzig, Lower Saxony, Germany
  • 2 ScaDS.AI Leipzig, Leipzig, Lower Saxony, Germany

The final, formatted version of the article will be published soon.

    Sequence alignments are often used to analyze genomic data. However, such alignments are often only calculated and compared on small sequence intervals for analysis purposes. When comparing longer sequences, these are usually divided into shorter sequence intervals for better alignment results. This usually means that the order context of the original sequence is lost. To prevent this, it is possible to use a graph structure to represent the order of the original sequence on the alignment blocks. The visualization of these graph structures can provide insights into the structural variations of genomes in a semi-global context. In this paper, we propose a new graph drawing framework for representing gMSA data. We produce a hierarchical graph layout that supports the comparative analysis of genomes. Based on a reference, the differences and similarities of the different genome orders are visualized. In this work, we present a complete graph drawing framework for gMSA graphs together with the respective algorithms for each of the steps. Additionally, we provide a prototype and an example data set for analyzing gMSA graphs. Based on this data set, we demonstrate the functionalities of the framework using two examples.

    Keywords: genome analysis, multiple sequence alignment, graph drawing, visualization, genome comparison

    Received: 19 Dec 2023; Accepted: 08 Jul 2024.

    Copyright: © 2024 Schebera, Zeckzer and Wiegreffe. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Jeremias Schebera, Leipzig University, Leipzig, 04109, Lower Saxony, Germany

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.