Viral IRES Prediction System - a Web Server for Prediction of the IRES Secondary Structure In Silico

The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.内部核糖体进入位点（internal ribosomal entry site, IRES）可在真核细胞中作为帽非依赖型翻译起始位点发挥功能。IRES元件已被广泛应用为双顺反子表达载体的实用工具。当前的RNA二级结构预测程序无法精准预测潜在的IRES元件。本研究设计了病毒IRES预测系统（viral IRES prediction system, VIPS）以开展IRES二级结构预测工作。为获得更优异的IRES预测效果，VIPS可针对四类不同的IRES进行评估与预测，且具备更高的预测精度。VIPS整合了RNA二级结构预测、结构比对以及假结预测三类程序，形成三阶段的预测流程。VIPS的核心组件包括：通过最小自由能法预测局部RNA二级结构的RNAL fold程序、用于比对预测结构的RNA Align程序，以及用于计算假结结构的pknotsRG程序。本研究利用非翻译区（UTR）数据库、IRES数据库与病毒数据库对VIPS进行了性能评估，结果显示VIPS对第1、2、3、4类IRES的预测准确率分别为98.53%、90.80%、82.36%与80.41%。这款高效的IRES结构搜索方法将有力推动IRES相关研究的开展。VIPS的在线网页服务地址为http://140.135.61.250/vips/