omiXcore：一个用于预测蛋白质与大型 RNA 相互作用的网络服务器。
omiXcore: a web server for prediction of protein interactions with large RNA.
机构信息
Bioinformatics and Genomics, Gene Function and Evolution, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology.
Bioinformatics and Genomics, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
出版信息
Bioinformatics. 2017 Oct 1;33(19):3104-3106. doi: 10.1093/bioinformatics/btx361.
SUMMARY
Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled library for exploration of human long intergenic RNAs interactions and (iii) prediction of binding sites.
RESULTS
omiXcore was trained and tested on enhanced UV Cross-Linking and ImmunoPrecipitation data. The method discriminates interacting and non-interacting protein-RNA pairs and identifies RNA binding sites with Areas under the ROC curve > 0.80, which suggests that the tool is particularly useful to prioritize candidates for further experimental validation.
AVAILABILITY AND IMPLEMENTATION
omiXcore is freely accessed on the web at http://service.tartaglialab.com/grant_submission/omixcore.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
本文介绍了 omiXcore，这是一个用于计算蛋白质与大 RNA（>500 个核苷酸）结合的服务器。我们的网络服务器允许（i）使用无大小限制的蛋白质和 RNA 序列，（ii）探索人类长基因间 RNA 相互作用的预编译库，以及（iii）预测结合位点。
结果
omiXcore 是在增强的 UV 交联和免疫沉淀数据上进行训练和测试的。该方法可区分相互作用和非相互作用的蛋白质-RNA 对，并识别 RNA 结合位点的 ROC 曲线下面积>0.80，这表明该工具特别有助于优先考虑候选者进行进一步的实验验证。
可用性和实现
omiXcore 可在 http://service.tartaglialab.com/grant_submission/omixcore 上免费访问。
联系方式
补充信息
补充数据可在 Bioinformatics 在线获得。
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