About






Background

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.

Conclusions

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.


Figure 1. Construction of small RNA illustration system.




Input sRNA raw sequencing fastq (10,096,827 reads, 1.5GB)
degradome raw sequencing fastq (62,546,911 reads, 6.7 GB)
host transcript fasta (265,363 transcripts, 243 MB)
virus genome fasta (2 genomes, 12.6 KB)
Output sRNA overview package: sRNA library statistics, miRNA and vsiRNA profiles
sRNA target package: sRNA-target profiles
Note: We also provide a web interface to illustrate all analysis results in figures and tables. All the outputs can be uploaded, and the results will be graphically represented.
Upload to website: http://sris.itps.ncku.edu.tw/status_check.php?E=Demo
Method FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit)
Bowtie (http://bowtie-bio.sourceforge.net/manual.shtml)
Personal Perl scripts
Running time 3 hours 21 minutes.