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Related Experiment Video

Updated: Jun 1, 2026

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
06:34

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

Published on: January 21, 2020

psRNATarget: a plant small RNA target analysis server.

Xinbin Dai1, Patrick Xuechun Zhao

  • 1Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.

Nucleic Acids Research
|May 31, 2011
PubMed
Summary

We developed psRNATarget, a plant small RNA target analysis tool. It accurately predicts microRNA and ta-siRNA targets, aiding gene regulatory network research.

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Area of Science:

  • Plant molecular biology
  • Bioinformatics
  • Genomics

Background:

  • Plant gene expression is regulated by small non-coding RNAs (20-24 nt), including microRNAs (miRNAs) and ta-siRNAs.
  • These small RNAs target transcription factors and development-related genes within gene regulatory networks (GRNs).
  • Existing target prediction tools are often designed for animal miRNAs, overlooking plant-specific recognition mechanisms.

Purpose of the Study:

  • To develop a specialized computational tool for analyzing plant microRNA and ta-siRNA targets.
  • To address the unique target recognition processes of plant small RNAs.

Main Methods:

  • Developed psRNATarget, a plant small RNA target analysis server.
  • Implemented reverse complementary matching with a scoring schema.
  • Incorporated target-site accessibility evaluation using unpaired energy (UPE).

Main Results:

  • psRNATarget distinguishes translational and post-transcriptional inhibition.
  • The tool reports potential small RNA binding activity based on target site pairs.
  • Designed for high-throughput analysis of next-generation sequencing data.

Conclusions:

  • psRNATarget provides a robust platform for plant small RNA target prediction.
  • The server facilitates efficient analysis of plant gene regulatory networks.
  • It is freely available online for researchers.

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Last Updated: Jun 1, 2026

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