miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.
miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.
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DOI：
10.1093/bioinformatics/btx210
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发表时间：
2017-08-15
期刊：
影响因子：
--
通讯作者：
Moxon S
中科院分区：
文献类型：
--
作者：
Paicu C;Mohorianu I;Stocks M;Xu P;Coince A;Billmeier M;Dalmay T;Moulton V;Moxon S
microrna是一类从稳定的发夹状二级结构中切除的~ 21 - 22nt小rna。它们具有重要的基因调控功能，参与真核生物的发育时序、器官发生和发育等多种途径。有几种计算工具用于下一代测序数据集的miRNA检测。然而，这些工具中的许多都有很高的假阳性和假阴性率。在这里，我们提出了一种新的miRNA预测算法，miRCat2。miRCat2结合了一种新的基于熵的方法来检测miRNA位点，该方法旨在应对当前下一代测序数据集的高测序深度。它具有用户友好的界面，并产生发夹结构的图形表示和描绘二级结构上序列对齐的绘图。我们在许多动物和植物数据集上测试了miRCat2，并与miRCat、miRDeep2、miRPlant和miReap进行了比较分析。我们还使用miRNA生物发生途径中的突变体来评估这些工具的预测。结果表明，与其他测试方法相比，miRCat2具有更高的准确性。此外，miRCat2预测了几种新的miRNA在野生型和突变型miRNA生物发生途径中的差异表达。miRCat2是UEA小RNA工作台的一部分，可以从http://srna-workbench.cmp.uea.ac.uk/免费获得。补充数据可在生物信息学网站获得。
MicroRNAs are a class of ∼21–22 nt small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current next-generation sequencing datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure. We test miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wild-type versus mutants in the miRNA biogenesis pathway. miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srna-workbench.cmp.uea.ac.uk/. Supplementary data are available at Bioinformatics online.
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影响因子：
3
作者：
An J;Lai J;Sajjanhar A;Lehman ML;Nelson CC
通讯作者：
Nelson CC
影响因子：
16
作者：
Bosson, Andrew D.;Zamudio, Jesse R.;Sharp, Phillip A.
通讯作者：
Sharp, Phillip A.
影响因子：
4.5
作者：
Cai, XZ;Hagedorn, CH;Cullen, BR
通讯作者：
Cullen, BR
DOI：
10.1126/science.1190809
发表时间：
2010-06-25
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Cifuentes D;Xue H;Taylor DW;Patnode H;Mishima Y;Cheloufi S;Ma E;Mane S;Hannon GJ;Lawson ND;Wolfe SA;Giraldez AJ
通讯作者：
Giraldez AJ
影响因子：
5.8
作者：
Bonnet, E;Wuyts, J;Van de Peer, Y
通讯作者：
Van de Peer, Y