Suárez-Quintana Clara, Navarro-Padilla Mar, Chorostecki Uciel, Sanchez Mayka
Department of Biomedicine, Iron metabolism: Regulation and Diseases Group, Universitat Internacional de Catalunya (UIC), Sant Cugat del Vallès 08195, Spain.
Department of Biomedicine, Computational RNA Biology Group, Universitat Internacional de Catalunya (UIC), Sant Cugat del Vallès 08195, Spain.
Nucleic Acids Res. 2025 Jul 7;53(W1):W520-W527. doi: 10.1093/nar/gkaf390.
Iron-responsive elements (IREs) are cis-acting regulatory RNA motifs that bind to iron regulatory proteins (IRP1 and IRP2), playing an essential role in the post-transcriptional regulation of genes involved in iron metabolism. Disruptions in this IRP/IRE regulatory system have been linked to several human diseases. SIREs (searching for IREs) is a web-server tool designed to predict IREs in nucleotide sequences. Here, we present SIREs 3.0 webserver, an improved new version built on a Flask-based framework, replacing the previous Perl backend to improve interconnectivity with other services. This upgrade introduces three novel input methods-batch, transcript, and gene modes-to cover researchers' needs, from large-scale analysis to single-gene queries. By integrating with NCBI and Ensembl APIs, SIREs 3.0 fetches genomic data to improve predictions with novel features, such as the location of the IREs in the transcript. Other novelties include novel IRE motifs based on in vivo verified data, broadening the scope of IRE detection. The scoring system has been refined with empirical data and enhanced graphical representations of predicted IREs have been added to the output. The interface is now more responsive and accessible across all devices. SIREs 3.0 can be accessed at: https://www.sires-webserver.eu.
铁反应元件（IREs）是一种顺式作用的调控RNA基序，可与铁调节蛋白（IRP1和IRP2）结合，在参与铁代谢的基因的转录后调控中发挥重要作用。这种IRP/IRE调节系统的破坏与多种人类疾病有关。SIREs（搜索IREs）是一种用于预测核苷酸序列中IREs的网络服务器工具。在此，我们展示了SIREs 3.0网络服务器，这是一个基于Flask框架构建的改进版本，取代了之前的Perl后端，以提高与其他服务的互连性。此次升级引入了三种新颖的输入方法——批量、转录本和基因模式——以满足研究人员从大规模分析到单基因查询的需求。通过与NCBI和Ensembl API集成，SIREs 3.0获取基因组数据，以利用诸如IREs在转录本中的位置等新特性改进预测。其他新特性包括基于体内验证数据的新型IRE基序，拓宽了IRE检测范围。评分系统已根据经验数据进行了优化，并在输出中添加了预测IREs的增强图形表示。现在界面响应更快，在所有设备上都可访问。可通过以下网址访问SIREs 3.0：https://www.sires-webserver.eu。
