ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
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DOI：
10.1093/bioinformatics/btl430
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发表时间：
2006-10-15
期刊：
影响因子：
5.8
通讯作者：
Baranov, Pavel V.
中科院分区：
文献类型：
--
作者：
Bekaert, Michael;Atkins, John F.;Baranov, Pavel V.
细菌基因组中编码释放因子的基因的正确注释通常因在释放因子 2 RF2 合成过程中使用 +1 程序化核糖体移码而变得复杂。在缺乏预测核糖体移码的强大计算方法的情况下，正确注释的成功取决于注释者对这种现象的熟悉程度。在这里，我们描述了一种新型计算机工具，可以自动区分编码 I 类细菌释放因子 RF1、RF2 和 RFH 的基因。最有用的是，该程序识别并自动注释 RF2 编码基因中的 +1 移码。 ARFA 性能与细菌基因组现有注释的比较表明，只有 20% 在表达过程中利用核糖体移码的 RF2 基因被正确注释。
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.