miRseqViewer – Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data

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). A team led by researchers from the Korean Institute of Bioscience and Biotechnology 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.

rna-seq

Availability: miRseqViewer, implemented in Java, is available at https://github.com/insoo078/mirseqviewer or at http://msv.kobic.re.kr

Contact: [email protected]

Jang I, Chang H, Jun Y, Park S, Yang JO, Lee B, Kim W, Kim VN, Lee S. (2014) miRseqViewer: Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data. Bioinformatics [Epub ahead of print]. [abstract]

 

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