# RepetDB: A TE database

Nicolas Francillonne, Mariène Wan, Nathalie Choisne, Françoise Alfama, Raphaël Flores, Joelle Amselem, Johann Confais, Hadi Quesneville

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## ► To cite this version:

Nicolas Francillonne, Mariène Wan, Nathalie Choisne, Françoise Alfama, Raphaël Flores, et al. RepetDB: A TE database. International congress on transposable elements ICTE, Apr 2024, Saint Malo, France. hal-04570060

HAL Id: hal-04570060

https://hal.science/hal-04570060

Submitted on 6 May 2024

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Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. Their detection and annotation are considered essential and must be undertaken in any genome sequencing project.

To annotate transposable elements in genome, consensus are needed and RepetDB aims to make available these sequence to make easier the annotation of closely related genomes. You can select consensus of interest in the database and download fasta sequence.

* I have an interesting sequence that I suspect is a transposable element and I wish to check if a match exist in the database. I go to PlantbioinfoPF blast services https://urgi.versailles.inrae.fr/blast/ and select in group « Repeats » a close related species

* I wish to make an annotation of a Brassicaceae species close from *Arabidopsis thaliana*. - I go to repetdb website and check the related species of interest https://urgi.versailles.inrae.fr/repetdb

<figure><img src="image_1.png" /></figure>

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* If a match is found I get a direct link to the consensus card

* I can also select multiple species, from example all *Brassicaceae* or just one close related species like *Arabidopsis thaliana*

<figure><img src="image_3.png" /></figure>

* Selection of specifics class, order or superfamily is also available to refine a search

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

Consensus search result

<figure><img src="image_5.png" /></figure>

* I can obtain statistics and filter some values out or download my result and consensus **fasta sequences**

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

By selecting one consensus I can access a consensus card describing its classification

<figure><img src="image_7.png" /></figure>

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

Visit RepetDB :

https://urgi.versailles.inrae.fr/repetdb/begin.do

Use URGI Blast :

https://urgi.versailles.inrae.fr/blast/

Supplementary information and tutorials :

https://urgi.versailles.inrae.fr/Data/Transposable-elements/REPETDB
Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. Their detection and annotation are considered essential and must be undertaken in any genome sequencing project.

To annotate transposable elements in genome, consensus are needed and RepetDB aims to make available these sequence to make easier the annotation of closely related genomes. You can select consensus of interest in the database and download fasta sequence.

* I wish to make an annotation of a Brassicaceae species close from *Arabidopsis thaliana*. - I go to repetdb website and check the related species of interest https://urgi.versailles.inrae.fr/repetdb

* I have an interesting sequence that I suspect is a transposable element and I wish to check if a match exist in the database. I go to PlantbioinfoPF blast services https://urgi.versailles.inrae.fr/blast/ and select in group « Repeats » a close related species

<figure><img src="image_3.png" /></figure>

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

* I can also select multiple species, from example all Brassicaceae or just one close related species like *Arabidopsis thaliana*

<figure><img src="image_5.png" /></figure>

* Selection of specifics class, order or superfamily is also available to refine a search

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

Consensus search result

<figure><img src="image_7.png" /></figure>

* I can obtain statistics and filter some values out or download my result and consensus **fasta sequences**

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

By selecting one consensus I can access a consensus card describing its classification

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

<figure><img src="image_10.png" /></figure>

Visit RepetDB :

https://urgi.versailles.inrae.fr/repetdb/begin.do

Use URGI Blast :

https://urgi.versailles.inrae.fr/blast/

Supplementary information and tutorials :

https://urgi.versailles.inrae.fr/Data/Transposable-elements/REPETDB