Construction of small RNA illustration system
Small RNA (sRNA) is shorter than 200 nt and containg different types. Some of them like microRNA (miRNA) and short interfering RNA (siRNA) are well-known for inducing degradation of messenger RNA (mRNA). Based on this mechanism, sRNA is an important regulator for controlling gene expression. Recently, next-generation sequencing (NGS) is broadly applied to reveal regulatory pathways of sRNA in many researches. Numerous bioinformatics tools have been developed to analyze sRNA NGS data. Most of the tools focus on investigating the expression profiling of sRNA, but limit in further functional analysis. Though few of them provide some functional assay, it is hard to get useful information from their analysis outputs.
Methods and Results
In order to solve the problems mentioned above, a comprehensive and user-friendly system for small RNA next-generation sequencing data analysis was developed in this study. There are two packages in this system. One of the packages is for sRNA overview analysis, not only miRNA but also virus-derived small interfering RNA (vsiRNA) can be identified. The other one is for sRNA target prediction. The sRNA targets are predicted via theoretical calculation and experimental data such as degradome sequencing. Moreover, user-friendly graphical and tabular outputs are provided in the system.
This Small RNA Illustration System (sRIS) not only help user to comprehensively analyze NGS data of sRNA, but also provide easily interpretive outputs. With the useful information from the analysis outputs, it will be more convenient to discover the important regulatory mechanism of sRNA.
Plant Bioinformatics and Molecular Biology Laboratory
Institute of Tropical Plant Sciences and Microbiology
National Cheng Kung University
Prof. Wen-Chi Chang: email@example.com
PBMB Lab: firstname.lastname@example.org
Tel: +886-6-2757575 ext.58311
Address: (70101) No.1, University Road, Tainan City, Taiwan (R.O.C)
Copyright © Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan Taiwan.