DIMES, Università della Calabria, Via Pietro Bucci 41 C, Cosenza, Italy.
Department of Mathematics and Computer Science, Università degli Studi di Palermo, Via Archirafi 34, Palermo, Italy.
BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):124. doi: 10.1186/s12859-019-2696-6.
RNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs and the corresponding coding DNA sequences. Software tools successful for the search of genes in other organisms not always are able to correctly perform this task in plants organellar genomes. Moreover, the available software tools predicting RNA editing events utilise algorithms that do not account for events which may generate a novel start codon.
We present FEDRO, a Java software tool implementing a novel strategy to generate candidate Open Reading Frames (ORFs) resulting from Cytidine to Uridine (c→u) editing substitutions which occur in the mitochondrial genome (mtDNA) of a given input plant. The goal is to predict putative proteins of plants mitochondria that have not been yet annotated. In order to validate the generated ORFs, a screening is performed by checking for sequence similarity or presence in active transcripts of the same or similar organisms. We illustrate the functionalities of our framework on a model organism.
The proposed tool may be used also on other organisms and genomes. FEDRO is publicly available at http://math.unipa.it/rombo/FEDRO .
RNA 编辑是植物细胞器中基因表达的一个重要机制。它改变了遗传信息从 DNA 到蛋白质的直接传递，因为 RNA 与相应的编码 DNA 序列之间存在差异。在其他生物体中搜索基因的软件工具并不总是能够正确地在植物细胞器基因组中执行此任务。此外，可用的预测 RNA 编辑事件的软件工具利用的算法没有考虑到可能产生新起始密码子的事件。
我们提出了 FEDRO，这是一个 Java 软件工具，它实现了一种新策略，用于生成来自于线粒体基因组（mtDNA）中胞嘧啶到尿嘧啶（c→u）编辑替换的候选开放阅读框（ORF），这些替换发生在给定输入植物中。目标是预测尚未注释的植物线粒体的潜在蛋白质。为了验证生成的 ORF，通过检查相同或相似生物体的活性转录本中是否存在序列相似性或存在来进行筛选。我们在一个模型生物上说明了我们框架的功能。
该工具也可用于其他生物体和基因组。FEDRO 可在 http://math.unipa.it/rombo/FEDRO 上获得。
