ATtRACT-a database of RNA-binding proteins and associated motifs
ATtRACT-a database of RNA-binding proteins and associated motifs
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DOI：
10.1093/database/baw035
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发表时间：
2016-04-07
影响因子：
5.8
通讯作者：
Lara-Pezzi, Enrique
中科院分区：
文献类型：
--
作者：
Giudice, Girolamo;Sanchez-Cabo, Fatima;Lara-Pezzi, Enrique
RNA结合蛋白（RBP）在RNA转运、剪接、多聚腺苷酸化和稳定性等关键细胞过程中起着至关重要的作用。了解RBP和RNA之间的相互作用是提高我们对RNA加工，定位和调控的知识的关键。尽管近年来取得了进展，但缺乏一个统一的非冗余资源，其中包括关于实验验证的基序、限制性商业惯例和利用这些信息的综合工具的信息。在这里，我们开发了一个名为ATtRACT的数据库（可在http://attract.cnic.es上获得），该数据库汇编了370个RBP和1583个RBP共有结合基序的信息，其中192个在任何其他数据库中都不存在。为了填充ATtRACT，我们（i）从CISBP-RNA、SpliceAid-F、RBPDB数据库中提取并手工整理实验验证的数据，（ii）整合并更新不可用的ASD数据库，以及（iii）通过计算分析从蛋白质数据库中存在的蛋白质-RNA复合物中提取信息。ATtRACT还提供了有效的算法来搜索特定的基序，并一次扫描一个或多个RNA序列。它还允许发现在一组相关序列中富集的从头基序，并将它们与数据库中包含的基序进行比较。
RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available at http://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discovering de novo motifs enriched in a set of related sequences and compare them with the motifs included in the database.