ReFernment：一个用于注释质体基因组中RNA编辑的R软件包。
ReFernment: An R package for annotating RNA editing in plastid genomes.
作者信息
Robison Tanner A, Wolf Paul G
机构信息
Department of Biology Utah State University Logan Utah USA.
出版信息
Appl Plant Sci. 2019 Jan 30;7(2):e01216. doi: 10.1002/aps3.1216. eCollection 2019 Feb.
Abstract
PREMISE OF THE STUDY
In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts.
METHODS AND RESULTS
We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.
CONCLUSIONS
Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of plastome sequences for taxa with high levels of RNA editing.
摘要
研究前提
在没有互补DNA（cDNA）的情况下，质体基因组中RNA编辑的注释必须手动完成，这对于研究蕨类植物和角苔细胞器基因组的人员来说意味着巨大的时间成本。
方法与结果
我们开发了一个R软件包，用于自动注释质体基因组中明显的无义突变。该软件成功注释了此类位点，并且对于没有测序或组装错误的数据不会产生假阳性结果。
结论
与手动注释相比，ReFernment在注释RNA编辑位点方面具有更高的速度和准确性。该软件对于为具有高水平RNA编辑的分类群生成大量质体基因组序列的研究人员应该特别有用。
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