# A layout framework for genome-wide multiple sequence alignment graphs

## TL;DR

This paper introduces a new framework for visualizing genome-wide multiple sequence alignments using graph layouts to preserve sequence order context.

## Contribution

The novel contribution is a hierarchical graph layout framework for gMSA data that enables comparative genome analysis.

## Key findings

- A hierarchical graph layout was developed to visualize genome order differences and similarities.
- A prototype and example dataset demonstrate the framework's functionalities with two examples.

## Abstract

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.