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Related Experiment Video

Updated: May 10, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing.

Jinyu Wu¹, Qi Liu, Xin Wang

¹Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences; University of Science and Technology of China; Hefei, China; Institute of Genomic Medicine; Wenzhou Medical College; Wenzhou, China.

|June 20, 2013

Summary

The updated mirTools 2.0 software now detects and profiles diverse non-coding RNAs (ncRNAs), identifies their target genes, and analyzes differential expression. This tool enhances small RNA transcriptome research.

Keywords:

miRNA miRNA targets mirTools ncRNA next-generation sequencing web server

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Last Updated: May 10, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Published on: August 4, 2016

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Published on: May 1, 2021

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

Published on: September 16, 2019

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Next-generation sequencing (NGS) is crucial for cost-effective analysis of non-coding RNA (ncRNA) complexity.
Existing tools like mirTools 1.0 primarily focused on microRNA (miRNA) discovery and profiling.
A need exists for comprehensive analysis of various ncRNA types and their functions.

Purpose of the Study:

To introduce mirTools 2.0, an enhanced software for small RNA transcriptome analysis.
To expand ncRNA detection capabilities beyond miRNAs to include tRNAs, snRNAs, snoRNAs, rRNAs, and piRNAs.
To provide advanced functional annotation of miRNA targets and differential expression analysis for multiple ncRNA types.

Main Methods:

Development of mirTools 2.0, an updated version of the original mirTools software.
Integration of modules for detecting and profiling diverse ncRNA classes (miRNA, tRNA, snRNA, snoRNA, rRNA, piRNA).
Implementation of functions for identifying miRNA-targeted genes, performing functional annotation (Gene Ontology, KEGG, PPI), and detecting differential expression.

Main Results:

mirTools 2.0 supports the detection and profiling of multiple ncRNA types.
The software identifies miRNA targets and performs detailed functional annotation.
Differential expression analysis for ncRNAs is now possible between two or more experimental groups.
Improved strategies for novel miRNA and piRNA detection and expanded taxonomy support are included.

Conclusions:

mirTools 2.0 offers a comprehensive solution for small RNA transcriptome analysis.
The enhanced features provide deeper insights into ncRNA functions and regulatory networks.
This tool will significantly aid researchers in studying small RNA biology.