miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data.
miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data.
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DOI：
10.1186/1471-2105-15-275
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发表时间：
2014-08-12
影响因子：
3
通讯作者：
Nelson CC
中科院分区：
文献类型：
--
作者：
An J;Lai J;Sajjanhar A;Lehman ML;Nelson CC
小型RNA测序通常用于识别新型miRNA，并确定植物中的几种miRNA鉴定工具，例如Mirdeep，Mirdeep2和Mirdeep*。预测新型的植物miRNA，同时提供具有提高预测准确性的用户友好界面。
我们已经开发了一种称为mirplant的用户友好的植物miRNA预测工具。图表。
我们开发了米尔德普（Mirplant），通过采用合适的策略来识别植物的发夹意外区域和发夹结构过滤特征将使生物学家能够可视化新型的MIRNA结构，并且相对于发夹的小RNA读取的位置。
Mirplant及其手册免费提供，请访问http://www.australianprostatecentre.org/research/software/mirplant或http://sourceforge.net/projects/projects/mirplant/。
本文的在线版本（DOI：10.1186/1471-2105-15-275）包含补充材料，可供授权用户使用。
Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills. miRPlant and its manual are freely available at http://www.australianprostatecentre.org/research/software/mirplant or http://sourceforge.net/projects/mirplant/. The online version of this article (doi:10.1186/1471-2105-15-275) contains supplementary material, which is available to authorized users.
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microRNA分析：方法和考虑因素。
DOI：
10.1038/nrg3198
发表时间：
2012-04-18
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Pritchard CC;Cheng HH;Tewari M
通讯作者：
Tewari M
影响因子：
7
作者：
Zhu, Qian-Hao;Spriggs, Andrew;Helliwell, Chris
通讯作者：
Helliwell, Chris
影响因子：
5.8
作者：
Yang, Xiaozeng;Li, Lei
通讯作者：
Li, Lei
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
46.9
作者：
Friedlaender, Marc R.;Chen, Wei;Rajewsky, Nikolaus
通讯作者：
Rajewsky, Nikolaus