Molecular BioMedicine Program, Research Centre, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia.
Nucleic Acids Res. 2018 Jan 4;46(D1):D218-D220. doi: 10.1093/nar/gkx975.
Here we present an updated version of the AU-Rich Element Database (ARED-Plus) that is freely available at http://brp.kfshrc.edu.sa/ared. AREs are conserved sequence elements that were first discovered in the 3'UTR of mammalian transcripts. Over the past years, we compiled a series of ARE databases that revealed the extent and wide distribution of ARE-containing genes. For this update, we adopted an optimized search algorithm with improved specificity and sensitivity in ARE selection. The designation of the different ARE clusters was simplified by directly correlating the number of the ARE cluster to the number of overlapping AUUUA pentamers. Additionally, the new database was expanded to include genes with intronic AREs (pre-mRNAs) and their characteristics since recent observations reported their abundance and biological significance. Several enhancements were incorporated such as customized column view, additional search options and live search functionalities. The new version includes links to AREsite and AREScore, two related ARE assessment algorithms for further evaluation of the ARE characteristics. ARED-Plus now contains an updated repertoire of AREs in the human transcriptome that may be useful in several research fields.
在这里，我们呈现了一个经过更新的 AU-Rich 元素数据库（ARED-Plus），它可以在 http://brp.kfshrc.edu.sa/ared 上免费获取。AREs 是保守的序列元件，最初在哺乳动物转录本的 3'UTR 中被发现。在过去的几年中，我们编写了一系列的 ARE 数据库，揭示了含有 ARE 的基因的广泛程度和分布。对于此次更新，我们采用了一种优化的搜索算法，提高了 ARE 选择的特异性和敏感性。通过将 ARE 簇的数量与重叠 AUUUA 五聚体的数量直接相关联，简化了不同 ARE 簇的指定。此外，新数据库扩展到包括具有内含子 AREs（前体 mRNA）及其特征的基因，因为最近的观察报告显示了它们的丰度和生物学意义。还整合了一些增强功能，例如自定义列视图、附加搜索选项和实时搜索功能。新版本包括到 AREsite 和 AREScore 的链接，AREScore 是两个用于进一步评估 ARE 特征的相关 ARE 评估算法。ARED-Plus 现在包含了人类转录组中更新的 ARE 库，这在几个研究领域可能会很有用。
