Bekaert Michaël, Atkins John F, Baranov Pavel V
Biosciences Institute, University College Cork, Cork, Ireland.
Bioinformatics. 2006 Oct 15;22(20):2463-5. doi: 10.1093/bioinformatics/btl430. Epub 2006 Aug 7.
Correct annotation of genes encoding release factors in bacterial genomes is often complicated by utilization of +1 programmed ribosomal frameshifting during synthesis of release factor 2, RF2. In the absence of robust computational approaches for predicting ribosomal frameshifting, the success of proper annotation depends on annotators' familiarity with this phenomenon. Here we describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly.
The PHP based web interface of ARFA and the source code are located at http://recode.genetics.utah.edu/arfa
在细菌基因组中，编码释放因子的基因的正确注释常常因在释放因子2（RF2）合成过程中使用+1程序性核糖体移码而变得复杂。在缺乏用于预测核糖体移码的强大计算方法的情况下，正确注释的成功与否取决于注释者对这一现象的熟悉程度。在此，我们描述了一种新型计算机工具，它能够自动区分编码I类细菌释放因子RF1、RF2和RFH的基因。最有用的是，该程序能够识别并自动注释RF2编码基因中的+1移码。将ARFA的性能与细菌基因组的现有注释进行比较发现，在其表达过程中利用核糖体移码的RF2基因中，只有20%得到了正确注释。
基于PHP的ARFA网络界面和源代码位于http://recode.genetics.utah.edu/arfa
