Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
Sci Rep. 2022 Oct 20;12(1):17588. doi: 10.1038/s41598-022-21732-0.
Nucleic acid motifs consist of conserved and variable nucleotide regions. For functional action, several motifs are combined to modules. The tool AIModules allows identification of such motifs including combinations of them and conservation in several nucleic acid stretches. AIModules recognizes conserved motifs and combinations of motifs (modules) allowing a number of interesting biological applications such as analysis of promoter and transcription factor binding sites (TFBS), identification of conserved modules shared between several gene families, e.g. promoter regions, but also analysis of shared and conserved other DNA motifs such as enhancers and silencers, in mRNA (motifs or regulatory elements e.g. for polyadenylation) and lncRNAs. The tool AIModules presented here is an integrated solution for motif analysis, offered as a Web service as well as downloadable software. Several nucleotide sequences are queried for TFBSs using predefined matrices from the JASPAR DB or by using one's own matrices for diverse types of DNA or RNA motif discovery. Furthermore, AIModules can find TFBSs common to two or more sequences. Demanding high or low conservation, AIModules outperforms other solutions in speed and finds more modules (specific combinations of TFBS) than alternative available software. The application also searches RNA motifs such as polyadenylation site or RNA-protein binding motifs as well as DNA motifs such as enhancers as well as user-specified motif combinations ( https://bioinfo-wuerz.de/aimodules/ ; alternative entry pages: https://aimodules.heinzelab.de or https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/aimodules ). The application is free and open source whether used online, on-site, or locally.
核酸基序由保守和可变核苷酸区域组成。为了发挥功能，几个基序组合成模块。AIModules 工具可识别这些基序，包括它们的组合以及在几个核酸序列中的保守性。AIModules 识别保守基序和基序组合（模块），允许进行许多有趣的生物学应用，例如分析启动子和转录因子结合位点 (TFBS)、识别几个基因家族之间共享的保守模块，例如启动子区域，还可以分析共享和保守的其他 DNA 基序，如增强子和沉默子，在 mRNA（基序或调控元件，例如用于多聚腺苷酸化）和 lncRNA 中。这里介绍的 AIModules 工具是一种用于基序分析的集成解决方案，既提供 Web 服务，也提供可下载的软件。使用 JASPAR DB 中的预定义矩阵或自己的矩阵，对几个核苷酸序列进行 TFBS 查询，用于各种类型的 DNA 或 RNA 基序发现。此外，AIModules 可以找到两个或更多序列共有的 TFBS。要求高或低的保守性，AIModules 在速度上优于其他解决方案，并且比其他可用软件发现更多的模块（TFBS 的特定组合）。该应用程序还搜索 RNA 基序，如多聚腺苷酸化位点或 RNA-蛋白质结合基序，以及 DNA 基序，如增强子以及用户指定的基序组合（https://bioinfo-wuerz.de/aimodules/; 替代入口页面：https://aimodules.heinzelab.de 或 https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/aimodules）。无论在线使用、现场使用还是本地使用，该应用程序都是免费和开源的。
