# Annotation transfer in pangenome graphs

Nina Marthe

► To cite this version:

Nina Marthe. Annotation transfer in pangenome graphs. XI JORNADES DE BIOINFORMÀTICA I GENÒMICA, Dec 2023, Barcelone, Spain. hal-04490506v2

HAL Id: hal-04490506

https://hal.science/hal-04490506v2

Submitted on 23 Jul 2025

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# Annotation transfer in pangenome graphs

Nina Marthe, nina.marthe@ird.fr

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PROGRAMME
DE RECHERCHE
---
AGROÉCOLOGIE
ET NUMÉRIQUE

Annotation transfer usually consists in aligning the annotated sequences on the genome we want to transfer to. This approach can be applied to pangenome graphs, however it sacrifices precision to reduce runtime. Pangenome graphs allow another approach for annotation transfer that doesn't rely on alignment, since it simply converts the annotated region's coordinates to get their position in the graph.

## Traditional annotation transfer

<figure><img src="image_4.png" /></figure>

* Approximate solution (heuristic solution)

* Sacrifices precision to reduce runtime

## Annotation transfer using coordinate conversion

<figure><img src="image_5.png" /><figcaption>Annotation transfer from graph to genome</figcaption></figure>

<figure><img src="image_6.png" /></figure>

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<figure><img src="image_8.png" /></figure>

* High precision (exact solution)

* No sequence information needed

* Uses simple operations

<figure><img src="image_9.png" /></figure>

* High precision (exact solution)

* Cannot miss a part of the gene

* Can detect modifications of the gene

## Comparison with Liftoff transfer

<figure><img src="image_10.png" /><figcaption>Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations.</figcaption></figure>

## Indel distribution in genes

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

Implemented in python
within GrAnnoT

This new approach provides an exact solution to annotation transfer. It should prove valuable to both genome and pangenome studies, and allow for a better harnessing of the information contained within the pangenomes.