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sRIS: A Small RNA Illustration System for Plant Next-Generation Sequencing Data Analysis

sRIS: A Small RNA Illustration System for Plant Next-Generation Sequencing Data Analysis

Authors :
Chi Nga Chow
Yi Fan Chiang-Hsieh
Tzong-Yi Lee
Han Qin Zheng
Hsuan Pai
Nai Yun Wu
Wen Chi Chang
Kuan Chieh Tseng
Song Bin Chang
Na-Sheng Lin
Source :
Plant and Cell Physiology. 61:1204-1212
Publication Year :
2020
Publisher :
Oxford University Press (OUP), 2020.

Abstract

Small RNA (sRNA), such as microRNA (miRNA) and short interfering RNA, are well-known to control gene expression based on degradation of target mRNA in plants. A considerable amount of research has applied next-generation sequencing (NGS) to reveal the regulatory pathways of plant sRNAs. Consequently, numerous bioinformatics tools have been developed for the purpose of analyzing sRNA NGS data. However, most methods focus on the study of sRNA expression profiles or novel miRNAs predictions. The analysis of sRNA target genes is usually not integrated into their pipelines. As a result, there is still no means available for identifying the interaction mechanisms between host and virus or the synergistic effects between two viruses. For the present study, a comprehensive system, called the Small RNA Illustration System (sRIS), has been developed. This system contains two main components. The first is for sRNA overview analysis and can be used not only to identify miRNA but also to investigate virus-derived small interfering RNA. The second component is for sRNA target prediction, and it employs both bioinformatics calculations and degradome sequencing data to enhance the accuracy of target prediction. In addition, this system has been designed so that figures and tables for the outputs of each analysis can be easily retrieved and accessed, making it easier for users to quickly identify and quantify their results. sRIS is available at http://sris.itps.ncku.edu.tw/.

Details

ISSN :
14719053 and 00320781
Volume :
61
Database :
OpenAIRE
Journal :
Plant and Cell Physiology
Accession number :
edsair.doi.dedup.....4bda9c039d98d681fe3acf27295dc66d
Full Text :
https://doi.org/10.1093/pcp/pcaa034