Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Ke Karlovu, Praha.
Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences, Videnska, Praha.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz047.
Secondary data structure of RNA molecules provides insights into the identity and function of RNAs. With RNAs readily sequenced, the question of their structural characterization is increasingly important. However, RNA structure is difficult to acquire. Its experimental identification is extremely technically demanding, while computational prediction is not accurate enough, especially for large structures of long sequences. We address this difficult situation with rPredictorDB, a predictive database of RNA secondary structures that aims to form a middle ground between experimentally identified structures in PDB and predicted consensus secondary structures in Rfam. The database contains individual secondary structures predicted using a tool for template-based prediction of RNA secondary structure for the homologs of the RNA families with at least one homolog with experimentally solved structure. Experimentally identified structures are used as the structural templates and thus the prediction has higher reliability than de novo predictions in Rfam. The sequences are downloaded from public resources. So far rPredictorDB covers 7365 RNAs with their secondary structures. Plots of the secondary structures use the Traveler package for readable display of RNAs with long sequences and complex structures, such as ribosomal RNAs. The RNAs in the output of rPredictorDB are extensively annotated and can be viewed, browsed, searched and downloaded according to taxonomic, sequence and structure data. Additionally, structure of user-provided sequences can be predicted using the templates stored in rPredictorDB.
RNA 分子的二级结构为研究 RNA 的结构与功能提供了重要线索。由于 RNA 易于测序，其结构特征的研究变得愈发重要。然而，RNA 结构的获取极具挑战性。其实验鉴定要求极高的技术水平，而计算预测又不够准确，特别是针对长序列的大型结构。rPredictorDB 是一个 RNA 二级结构的预测数据库，旨在填补 PDB 中实验鉴定结构和 Rfam 中预测的保守二级结构之间的空白。该数据库包含使用基于模板的 RNA 二级结构预测工具预测的个别二级结构，预测所基于的模板是具有至少一个实验解析结构的同源物的 RNA 家族的同源物。实验鉴定的结构被用作结构模板，因此预测的可靠性高于 Rfam 中的从头预测。序列从公共资源下载。目前，rPredictorDB 涵盖了 7365 个具有二级结构的 RNA。二级结构的图形使用 Traveler 包进行显示，以便于阅读具有长序列和复杂结构的 RNA，例如核糖体 RNA。rPredictorDB 输出的 RNA 经过广泛注释，可根据分类学、序列和结构数据进行查看、浏览、搜索和下载。此外，还可以使用 rPredictorDB 中存储的模板预测用户提供的序列的结构。
