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Related Experiment Video

Updated: Feb 13, 2026

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

Published on: January 21, 2020

P-GRe: An efficient pipeline for pseudogenes annotation.

Sébastien Cabanac¹, Christophe Dunand¹, Catherine Mathé¹

¹Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France.

|February 11, 2026

Summary

This summary is machine-generated.

Pseudogenes, once dismissed as "junk DNA", are now recognized for regulating genes. A new automated tool, Pseudo-Gene Retriever (P-GRe), enhances pseudogene identification and annotation across whole genomes.

Keywords:

Annotation Bioinformatics Pseudogene Software

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Pseudogenes were historically considered non-functional DNA.
Emerging research highlights their crucial roles in post-transcriptional gene regulation.
Pseudogene identification aids in understanding gene evolution and multigene family dynamics.

Purpose of the Study:

To develop a fully automated pipeline for whole-genome pseudogene annotation.
To introduce Pseudo-Gene Retriever (P-GRe), a novel software for pseudogene prediction.
To improve upon existing methods for pseudogene identification sensitivity and scope.

Main Methods:

Developed P-GRe, an automated pseudogene prediction tool.
Integrated the high-speed and sensitive aligner miniprot.
Implemented filtering and post-analysis steps for enhanced accuracy.

Main Results:

P-GRe provides a fully automated pseudogene annotation pipeline.
The software requires only genome sequence, GFF, and protein sequence files.
P-GRe demonstrates superior performance compared to existing software, with increased sensitivity.

Conclusions:

P-GRe offers a significant advancement in automated pseudogene annotation.
The tool enhances the capacity for identifying unitary pseudogenes.
This facilitates deeper insights into gene regulation and evolutionary processes.