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Section: Genomics
Topic: Genetics/Genomics

Pipeline to detect the positional and directional relationship between transposable elements and adjacent genes in host genome

Meguerditchian, Caroline1; Ergun, Ayse1; Decroocq, Veronique1 ; Lefebvre, Marie1  ; Bui, Quynh-Trang1  
1 UMR 1332 Biologie du Fruit et Pathologie, INRAE, University of Bordeaux, UMR BFP, Villenave-d’Ornon, France

10.24072/pcjournal.57 - Peer Community Journal, Volume 1 (2021), article no. e48.

Get full text PDF Peer reviewed and recommended by PCI

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 which is capable to reveal the positional and directional relationship between TEs and adjacent gene distribution in the host genome. Our tool is freely available here: https://github.com/marieBvr/TEs_genes_relationship_pipeline

Published online:
DOI: 10.24072/pcjournal.57
Type: Software tool
Meguerditchian, Caroline 1; Ergun, Ayse 1; Decroocq, Veronique 1; Lefebvre, Marie 1; Bui, Quynh-Trang 1

1 UMR 1332 Biologie du Fruit et Pathologie, INRAE, University of Bordeaux, UMR BFP, Villenave-d’Ornon, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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     title = {Pipeline to detect the positional and directional relationship between transposable elements and adjacent genes in host genome},
     journal = {Peer Community Journal},
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Meguerditchian, Caroline; Ergun, Ayse; Decroocq, Veronique; Lefebvre, Marie; Bui, Quynh-Trang. Pipeline to detect the positional and directional relationship between transposable elements and adjacent genes in host genome. Peer Community Journal, Volume 1 (2021), article  no. e48. doi : 10.24072/pcjournal.57. https://peercommunityjournal.org/articles/10.24072/pcjournal.57/

Peer reviewed and recommended by PCI : 10.24072/pci.genomics.100010

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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