Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). We present a highly interactive application that visualizes the sequence alignment, secondary structure and normalized read counts in synchronous multi-panel windows. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products and thereby will facilitate the studies on miRNA biogenesis and regulation. The project manager handles multiple samples of multiple groups. The read alignment is imported in BAM file format. Implemented features comprise sorting, zooming, highlighting, editing, filtering, saving, exporting, etc. Currently, miRseqViewer supports 84 organisms whose annotation is available at miRBase.

• Synchronized multi-panel visualization to show short read alignment, secondary structure of microRNA, and read count table. This helps users to easily examine the relationships between the structure of precursor and the sequences and abundance of final products.
• Support of 84 organisms in the miRBase database. MicroRNA sequencing data from most organisms can be analyzed. We also support novel microRNAs not included in the miRBase.
• Project manager handling multiple samples of multiple groups. Users can compare differential processing of pre-miRNAs in different contexts such as normal and tumor samples.
• Portable and light installation. miRseqViewer requires Java JDK 1.6 only with no other software or library. It runs in most operating systems including Mac, Windows, and Linux.
• A number of user-friendly interactive features. We implemented diverse features such as read filtering, sorting, editing, exporting and importing, and four normalization methods.