title: StarScan: a web server for scanning small RNA targets from degradome sequencing data.
abstract: Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/.
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China.
authors.forename: Shun
authors.initials: S
authors.lastname: Liu
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China.
authors.forename: Jun-Hao
authors.initials: JH
authors.lastname: Li
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wu
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China.
authors.forename: Ke-Ren
authors.initials: KR
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P. R. China lssqlh@mail.sysu.edu.cn.
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Yang
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P. R. China lssqlh@mail.sysu.edu.cn.
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
mesh_terms: D000818:Animals; D006801:Humans; D020407:Internet; D059367:RNA Cleavage; D018749:RNA, Plant / Q000737:chemistry / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D018749:RNA, Plant; D058727:RNA, Small Untranslated