P-GRe : an efficient pipeline to maximised pseudogene prediction in plants/eucaryotes - Université Toulouse III - Paul Sabatier - Toulouse INP Accéder directement au contenu
Pré-Publication, Document De Travail (Preprint/Prepublication) Année : 2023

P-GRe : an efficient pipeline to maximised pseudogene prediction in plants/eucaryotes

Résumé

Formerly considered as part of "junk DNA", pseudogenes are nowadays known for their role in the post-transcriptional regulation of functional genes. In addition, their identification allows a better understanding of gene evolution in the frame of multigenic families. Despite this, there is, to our knowledge, no fully automatic user-friendly software allowing the annotation of pseudogenes on a whole genome. Here, we present Pseudo-Gene Retriever (P-GRe), a fully automated pseudogene prediction software requiring only a genome sequence and its corresponding GFF annotation file. P-GRe detects the sequences of the pseudogenes on a whole genome and returns to the user all their genomic sequences and their pseudo-coding sequences. The ability of P-GRe to finely reconstruct the structure of pseudogenes also allow to obtain a set of proteins virtually encoded by the predicted pseudogenes. We show here that in 70% of the cases, virtual proteins constructed by P-GRe from Arabidopsis thaliana proteome and genome aligned better to their parent protein than their annotated counterpart.
Fichier principal
Vignette du fichier
Cabanac_2023.pdf (1.49 Mo) Télécharger le fichier
Origine Fichiers produits par l'(les) auteur(s)
Licence

Dates et versions

hal-04483163 , version 1 (29-02-2024)

Licence

Identifiants

Citer

Sébastien Cabanac, Christophe Dunand, Catherine Mathé. P-GRe : an efficient pipeline to maximised pseudogene prediction in plants/eucaryotes. 2024. ⟨hal-04483163⟩
21 Consultations
4 Téléchargements

Altmetric

Partager

Gmail Mastodon Facebook X LinkedIn More