mirTools: microRNA profiling and discovery based on high-throughput sequencing.
mirTools: microRNA profiling and discovery based on high-throughput sequencing.
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DOI：
10.1093/nar/gkq393
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发表时间：
2010-07
影响因子：
14.9
通讯作者：
Wu J
中科院分区：
文献类型：
--
作者：
Zhu E;Zhao F;Xu G;Hou H;Zhou L;Li X;Sun Z;Wu J
MiRNAs是一种小的、非编码的RNA，它在转录后水平负向调节基因的表达，在发育和肿瘤发生等各种生理和病理过程中发挥着至关重要的作用。尽管深度测序技术已经被应用于各种小RNA转录本的研究，但与基于微阵列的方法相比，它们的计算方法还远未成熟。在这项研究中，开发了一个全面的网络服务器mirTools，使研究人员能够全面地表征小RNA转录组。在mirTools的帮助下，用户可以：(I)从原始测序数据中筛选出低质量的读数和3/5‘接头；(Ii)将大规模的短读数与参考基因组比对并探索其长度分布；(Iii)将小RNA候选分类为已知的类别，如已知的miRNAs、非编码RNA、基因组重复序列和编码序列；(Iv)提供已知miRNAs的详细注释信息，如miRNA/miRNA*、绝对/相对读数和最丰富的标签；(V)预测以前尚未表征的新的miRNAs；以及(Vi)基于两种不同的计数策略来识别样本之间差异表达的miRNAs：总的读取标签计数和最丰富的标签计数。我们相信，在mirTool中集成多种计算方法将极大地促进当前以多种方式进行的microRNA研究。可以在http://centre.bioinformatics.zj.cn/mirtools/和http://59.79.168.90/mirtools.上访问MirTool
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.
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影响因子：
64.8
作者：
Lu, J;Getz, G;Golub, TR
通讯作者：
Golub, TR
deepBase：用于深度注释和挖掘深度测序数据的数据库
影响因子：
14.9
作者：
Yang JH;Shao P;Zhou H;Chen YQ;Qu LH
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影响因子：
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Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.
影响因子：
4.4
作者：
Wang W;Wang Y;Zhang Q;Qi Y;Guo D
通讯作者：
Guo D