Related Experiment Video
Updated: Apr 22, 2026
A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
Published on: August 21, 2019
miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing
Insu Jang1, Hyeshik Chang1, Yukyung Jun1
1Korean Bioinformation Center (KOBIC), KRIBB, Daejeon 305-806, Korea, School of Biological Sciences, Seoul National University, Seoul 151-742, Korea and Department of Life Science and Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul 120-750, Korea.
A new tool, miRseqViewer, allows simultaneous visualization of microRNA (miRNA) sequence, structure, and expression. This facilitates understanding miRNA biogenesis and regulation by linking precursor structure to final product sequences and abundance.
Area of Science:
- Bioinformatics
- Molecular Biology
- Genomics
Background:
- Deep sequencing of small RNAs is a common technique.
- Existing tools lack integrated visualization of miRNA sequence, secondary structure, and gene expression.
- Understanding the relationship between precursor structure and mature miRNA products is crucial for studying miRNA biogenesis and regulation.
Purpose of the Study:
- To introduce miRseqViewer, a novel interactive application for visualizing small RNA sequencing data.
- To enable simultaneous exploration of sequence features, secondary structure, and gene expression of microRNAs (miRNAs).
- To facilitate the examination of structure-sequence-abundance relationships in miRNA biogenesis and regulation studies.
Main Methods:
- Development of miRseqViewer, an interactive application implemented in Java.
- Visualization of sequence alignment (BAM format), secondary structure, and normalized read counts in synchronized multi-panel windows.
- Implementation of features including sorting, zooming, highlighting, editing, filtering, saving, and exporting.
Main Results:
- miRseqViewer provides a comprehensive platform for exploring miRNA data.
- The tool allows users to correlate precursor structure with mature miRNA sequences and their expression levels.
- Supports data from 84 organisms with annotations available at miRBase.
Conclusions:
- miRseqViewer addresses the need for a dedicated viewer for simultaneous analysis of miRNA sequence, structure, and expression.
- The application enhances the study of miRNA biogenesis and regulation by providing integrated visualization.
- Facilitates comparative analysis across multiple samples and groups for 84 organisms.
