文献类型：期刊文献

英文题名：Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing

作者：Liu, Qi[1] Ding, Changjun[1] Lang, Xiaoqiang[2] Guo, Ganggang[3] Chen, Jiafei[1] Su, Xiaohua[1,4,5]

第一作者：Liu, Qi

通信作者：Su, XH[1];Su, XH[2]

机构：[1]Chinese Acad Forestry, Res Inst Forestry, State Key Lab Tree Genet & Breeding, Beijing 100091, Peoples R China;[2]Sichuan Univ, West China Med Ctr, Chengdu, Peoples R China;[3]Chinese Acad Agr Sci, Inst Crop Sci, Beijing, Peoples R China;[4]Chinese Acad Forestry, Res Inst Forestry, Forest Tree Breeding, Beijing, Peoples R China;[5]Nanjing Forestry Univ, Coinnovat Ctr Sustainable Forestry Southern China, Nanjing, Peoples R China

年份：2021

卷号：22

期号：1

起止页码：463-473

外文期刊名：BRIEFINGS IN BIOINFORMATICS

收录：;Scopus(收录号：2-s2.0-85091952740);WOS:【SCI-EXPANDED(收录号:WOS:000634950200035)】；

基金：Basic Research Fund of RIF (Grant No. CAFYBB2017ZY006); TheNationalNatural Science Foundation of China (Grant No. 31870662).

语种：英文

外文关键词：small noncoding RNA; software; phasiRNA; tRF; 24-nt siRNA; wood formation

摘要：Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https:// bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.