SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.
SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.
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DOI：
10.1093/nar/gkt550
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发表时间：
2013-08
影响因子：
14.9
通讯作者：
Gladyshev VN
中科院分区：
文献类型：
--
作者：
Mariotti M;Lobanov AV;Guigo R;Gladyshev VN
硒蛋白是一种含有罕见氨基酸硒半胱氨酸(SEC)的蛋白质。SEC由一种特定的翻译机制插入，该机制识别硒蛋白基因3‘UTR处的茎环结构，即SECIS元件，并在编码序列中重新编码UGA密码子。由于UGA通常是一个翻译停止信号，硒蛋白通常被错误注释，必须为这类蛋白开发指定的工具。在这里，我们提出了两种新的计算方法，用于硒蛋白的鉴定和分析，我们通过http://gladyshevlab.org/SelenoproteinPredictionServer或http://seblastian.crg.es.的Web服务器公开提供了这两种方法SECISearch3取代其前身SECISearch成为预测真核细胞SECIS元件的工具。Seblastian是一种新的硒蛋白基因检测方法，它使用SECISearch3，然后预测SECIS元件上游编码的硒蛋白序列。塞布拉斯蒂安既能识别已知的硒蛋白，又能预测新的硒蛋白。通过将这些工具应用于不同的真核基因组，我们提供了一个新预测的硒蛋白及其注释的含半胱氨酸同源物的排序列表。对AhpC家族中一个有代表性的候选基因的分析表明，SEC在该蛋白中的使用是如何在细菌和真核生物谱系中进化的。
Selenoproteins are proteins containing an uncommon amino acid selenocysteine (Sec). Sec is inserted by a specific translational machinery that recognizes a stem-loop structure, the SECIS element, at the 3′ UTR of selenoprotein genes and recodes a UGA codon within the coding sequence. As UGA is normally a translational stop signal, selenoproteins are generally misannotated and designated tools have to be developed for this class of proteins. Here, we present two new computational methods for selenoprotein identification and analysis, which we provide publicly through the web servers at http://gladyshevlab.org/SelenoproteinPredictionServer or http://seblastian.crg.es. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. By applying these tools to diverse eukaryotic genomes, we provide a ranked list of newly predicted selenoproteins together with their annotated cysteine-containing homologues. An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages.
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影响因子：
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