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Related Experiment Video

Updated: Jun 18, 2025

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
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AmiR-P3: An AI-based microRNA prediction pipeline in plants.

Sobhan Ataei1, Jafar Ahmadi1, Sayed-Amir Marashi2

  • 1Department of Genetics and Plant Breeding, Imam Khomeini International University, Qazvin, Iran.

Plos One
|August 1, 2024
PubMed
Summary

A novel pipeline, AmiR-P3, predicts plant microRNAs (miRNAs) from genomic sequences without needing expression data. This tool aids in discovering conserved and novel miRNAs, especially in less-studied plant species.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • MicroRNAs (miRNAs) are crucial noncoding RNAs regulating gene expression post-transcriptionally in plants.
  • Existing miRNA prediction tools, often designed for animal sequences, face challenges with plant miRNA biogenesis complexity.
  • There is a need for computational methods to predict plant miRNAs directly from genomic sequences.

Purpose of the Study:

  • To develop a novel ab initio pipeline, AmiR-P3, for predicting plant microRNAs (miRNAs) from genomic sequences.
  • To create a flexible tool that allows users to adjust prediction criteria based on plant miRNA properties.
  • To enable miRNA prediction irrespective of expression levels or tissue specificity.

Main Methods:

  • AmiR-P3 pipeline identifies potential miRNA homologs, excluding protein-coding regions.
  • It computes RNA secondary structures using minimum free energy and employs a deep learning model for pre-miRNA prediction.
  • Final miRNA selection is based on a defined set of criteria.

Main Results:

  • The AmiR-P3 pipeline successfully predicts plant miRNAs from various species.
  • The method is effective in identifying both conserved and novel putative miRNAs.
  • Predictions are achieved without requiring sequencing reads or assembled reference genomes.

Conclusions:

  • AmiR-P3 facilitates miRNA prediction in diverse plant species, including those with limited genomic data.
  • The pipeline is adaptable for identifying miRNAs from any genomic or transcriptomic sequence.
  • AmiR-P3 is available as a portable Docker container for easy installation and use.