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Updated: May 21, 2026
09:29
A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
Published on: August 21, 2019
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments.
Ming Wen1, Yang Shen, Suhua Shi
1State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, People's Republic of China.
BMC Bioinformatics
|June 23, 2012
Summary
We developed miREvo, a new software tool, to analyze microRNA (miRNA) sequence and expression evolution across species using whole genome alignments. This helps understand miRNA functional dynamics and evolutionary relationships.
Area of Science:
- Evolutionary biology
- Bioinformatics
- Genomics
Background:
- MicroRNAs (miRNAs) are key non-coding RNAs regulating biological processes.
- Next-generation sequencing (NGS) is widely used for miRNA discovery.
- Limited computational tools exist for analyzing miRNA evolutionary dynamics across species.
Purpose of the Study:
- To develop an integrated software platform for analyzing miRNA sequence and expression evolution.
- To provide a tool for identifying novel miRNAs and their homologs across species.
- To facilitate the study of miRNA evolutionary dynamics.
Main Methods:
- Developed miREvo, a software platform with a graphical user interface (GUI).
- Utilized modified miRDeep algorithm for novel miRNA identification.
- Employed multiple-species whole genome alignments (WGAs) for evolutionary analysis.
- Analyzed small RNA sequencing data for miRNA expression profiling.
Main Results:
- miREvo identifies novel miRNAs in plants and animals.
- It detects miRNA homologs and calculates evolutionary distances using WGAs.
- The platform profiles miRNA expression and analyzes divergence across species.
- Demonstrated utility with Drosophila melanogaster and Arabidopsis data.
Conclusions:
- miREvo is an integrated pipeline for exploring miRNA expressional and evolutionary dynamics.
- The software is standalone, modular, and freely available.
- Facilitates cross-species miRNA research.
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