mirTools: microRNA profiling and discovery based on high-throughput sequencing

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	mirTools: microRNA profiling and discovery based on high-throughput sequencing
	Zhu, Erle 1,2; Zhao, Fangqing 3; Xu, Gang 2; Hou, Huabin 2; Zhou, LingLin 2; Li, Xiaokun 1; Sun, Zhongsheng2,4 ; Wu, Jinyu 2; Sun ZS(孙中生); Xiaokun Li ; Jinyu Wu
摘要	miRNAs are small, non-coding RNA that negatively regulate gene expression at post-transcriptional level, which play crucial roles in various physiological and pathological processes, such as development and tumorigenesis. Although deep sequencing technologies have been applied to investigate various small RNA transcriptomes, their computational methods are far away from maturation as compared to microarray-based approaches. In this study, a comprehensive web server mirTools was developed to allow researchers to comprehensively characterize small RNA transcriptome. With the aid of mirTools, users can: (i) filter low-quality reads and 3/5' adapters from raw sequenced data; (ii) align large-scale short reads to the reference genome and explore their length distribution; (iii) classify small RNA candidates into known categories, such as known miRNAs, non-coding RNA, genomic repeats and coding sequences; (iv) provide detailed annotation information for known miRNAs, such as miRNA/miRNA*, absolute/relative reads count and the most abundant tag; (v) predict novel miRNAs that have not been characterized before; and (vi) identify differentially expressed miRNAs between samples based on two different counting strategies: total read tag counts and the most abundant tag counts. We believe that the integration of multiple computational approaches in mirTools will greatly facilitate current microRNA researches in multiple ways. mirTools can be accessed at http://centre.bioinformatics.zj.cn/mirtools/ and http://59.79.168.90/mirtools.
学科领域	生理心理学/生物心理学
	2010-07-01
语种	英语
发表期刊	NUCLEIC ACIDS RESEARCH
ISSN	0305-1048
卷号	38 期号:1 页码:W392-W397
期刊论文类型	Article
收录类别	SCI
资助项目	一室原孙中生课题组
WOS记录号	WOS:000284148900062
引用统计	被引频次：98[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.psych.ac.cn/handle/311026/7249
专题	中国科学院心理研究所回溯数据库(1956-2010)
通讯作者	Sun ZS(孙中生); Xiaokun Li; Jinyu Wu
作者单位	1.Wenzhou Med Coll, Zhejiang Prov Key Lab Biotechnol Pharmaceut Engn, Sch Pharmaceut Sci, Wenzhou 325035, Peoples R China 2.Wenzhou Med Coll, Zhejiang Prov Key Lab Med Genet, Inst Genom Med, Wenzhou 325035, Peoples R China 3.Penn State Univ, Ctr Comparat Genom & Bioinformat, Dept Biochem & Mol Biol, University Pk, PA 16802 USA 4.Chinese Acad Sci, Inst Psychol, Behav Genet Ctr, Beijing 100101, Peoples R China
推荐引用方式 GB/T 7714	Zhu, Erle,Zhao, Fangqing,Xu, Gang,et al. mirTools: microRNA profiling and discovery based on high-throughput sequencing[J]. NUCLEIC ACIDS RESEARCH,2010,38(1):W392-W397.
APA	Zhu, Erle.,Zhao, Fangqing.,Xu, Gang.,Hou, Huabin.,Zhou, LingLin.,...&Jinyu Wu.(2010).mirTools: microRNA profiling and discovery based on high-throughput sequencing.NUCLEIC ACIDS RESEARCH,38(1),W392-W397.
MLA	Zhu, Erle,et al."mirTools: microRNA profiling and discovery based on high-throughput sequencing".NUCLEIC ACIDS RESEARCH 38.1(2010):W392-W397.

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