NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome
NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome
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DOI：
10.4061/2010/495904
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发表时间：
2010-09
影响因子：
2.3
通讯作者：
Jan-Hendrik Teune;G. Steger
中科院分区：
文献类型：
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作者：
Jan-Hendrik Teune;G. Steger
微小RNA（microRNA，miRNA）是一种非编码的小分子RNA，在真核生物基因组中转录为初级miRNA（pri-miRNA）。至少在植物中，它们的调节活性是通过与编码蛋白质的信使RNA（mRNA）的碱基配对介导的，随后是mRNA降解或翻译抑制。我们描述了NOVOMIR，一个用于鉴定植物基因组中miRNA基因的程序。它使用一系列过滤步骤和统计模型来区分前体miRNA与其他RNA，并且既不依赖于miRNA靶标的先验知识，也不依赖于比较基因组学。NOVOMIR检测拟南芥premiRNA的灵敏度和特异性分别为~0.83和~0.99。植物前体miRNA在大小和结构方面比动物前体miRNA更异质。尽管存在这些困难，NOVOMIR仍然非常适合在基因组规模上搜索前体miRNA。NOVOMIR是用Perl编写的，依赖于两个额外的免费程序来预测RNA二级结构（RNALFOLD，RNASHAPES）。
MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their regulatory activity is mediated through base-pairing with protein-coding messenger RNAs (mRNA) followed by mRNA degradation or translation repression. We describe NOVOMIR, a program for the identification of miRNA genes in plant genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA from other RNAs and does rely neither on prior knowledge of a miRNA target nor on comparative genomics. The sensitivity and specificity of NOVOMIR for detection of premiRNAs from Arabidopsis thaliana is ~0.83 and ~0.99, respectively. Plant pre-miRNAs are more heterogeneous with respect to size and structure than animal pre-miRNAs. Despite these difficulties, NOVOMIR is well suited to perform searches for pre-miRNAs on a genomic scale. NOVOMIR is written in Perl and relies on two additional, free programs for prediction of RNA secondary structure (RNALFOLD, RNASHAPES).