PCI Genomics

Title *

A pipeline to detect the relationship between transposable elements and adjacent genes in host genomesuse asterix (*) to get italics

Authors *

Caroline Meguerditchian, Ayse Ergun, Veronique Decroocq, Marie Lefebvre, Quynh-Trang BuiPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2021

Picture *

Abstract *

<p>Understanding the relationship between transposable elements (TEs) and their closest positional genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of their transcriptional activity. A comprehensive knowledge of structural organization between transposable elements and neighboring genes is important to study TE functional role in gene regulation. We implemented a pipeline to display the relationship between the distribution of TEs and adjacent genes in host genomes. Our tool is freely available here: https://github.com/marieBvr/TEs_genes_relationship_pipeline.</p>

Indicate the full web address (DOI or URL) giving public access to these data (if you have any problems with the deposit of your data, please contact contact@genomics.peercommunityin.org). In case all raw data are included in the preprint, indicate the DOI or URL of the preprint. *

https://www.ebi.ac.uk/ena/browser/view/PRJEB42606You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

Indicate the full web address (DOI or URL) giving public access to these scripts (if you have any problems with the deposit of your scripts, please contact contact@genomics.peercommunityin.org). In case all raw scripts are included in the preprint, indicate the DOI or URL of the preprint. *

https://www.rosaceae.org/node/10811682You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@genomics.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint. *

https://doi.org/10.5281/zenodo.4442377You should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Keywords (optional)

Transposable element, Gene, Genome, Bioinformatics, Pipeline

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Bioinformatics, Viruses and transposable elements

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Submission date

2021-03-03 15:08:34

Recommender

Emmanuelle Lerat

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