CROSSalive：一个用于预测 RNA 分子体内结构的网络服务器。
CROSSalive: a web server for predicting the in vivo structure of RNA molecules.
机构信息
Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.
Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
出版信息
Bioinformatics. 2020 Feb 1;36(3):940-941. doi: 10.1093/bioinformatics/btz666.
MOTIVATION
RNA structure is difficult to predict in vivo due to interactions with enzymes and other molecules. Here we introduce CROSSalive, an algorithm to predict the single- and double-stranded regions of RNAs in vivo using predictions of protein interactions.
RESULTS
Trained on icSHAPE data in presence (m6a+) and absence of N6 methyladenosine modification (m6a-), CROSSalive achieves cross-validation accuracies between 0.70 and 0.88 in identifying high-confidence single- and double-stranded regions. The algorithm was applied to the long non-coding RNA Xist (17 900 nt, not present in the training) and shows an Area under the ROC curve of 0.83 in predicting structured regions.
AVAILABILITY AND IMPLEMENTATION
CROSSalive webserver is freely accessible at http://service.tartaglialab.com/new_submission/crossalive.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
由于与酶和其他分子的相互作用，体内 RNA 结构难以预测。在这里，我们引入 CROSSalive，这是一种使用蛋白质相互作用预测来预测体内 RNA 的单链和双链区的算法。
结果
在存在（m6a+）和不存在 N6 甲基腺苷修饰（m6a-）的 icSHAPE 数据上进行训练，CROSSalive 在识别高可信度单链和双链区方面的交叉验证准确率在 0.70 到 0.88 之间。该算法应用于长非编码 RNA Xist（17900nt，不在训练中），在预测结构区域时，ROC 曲线下面积为 0.83。
可用性和实现
CROSSalive 网络服务器可在 http://service.tartaglialab.com/new_submission/crossalive 上免费访问。
补充信息
补充数据可在生物信息学在线获得。
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