miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data

• DOI: 10.1093/bioinformatics/btu676
• Publication Date: 2014-10-17T05:05:29Z
• Authors: Insu Jang; Hyeshik Chang; Yukyung Jun; Seongjin Park; Jin Ok Yang; Byungwook Lee; Wankyu Kim; V. Narry Kim; Sanghyuk Lee
• Keywords: 0301 basic medicine; MicroRNAs; 0303 health sciences; 03 medical and health sciences; Sequence Analysis, RNA; Computer Graphics; Computational Biology; High-Throughput Nucleotide Sequencing; Humans; Databases, Nucleic Acid; Sequence Alignment; Software

Summary: 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 multipanel 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. Availability and implementation: miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr. Contact: [e-mail]