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SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements

机译：SECISaln，基于Web的工具，用于创建基于结构的真核SECIS元素比对

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摘要

SUMMARY: Selenoproteins contain the 21st amino acid selenocysteine which is encoded by an inframe UGA codon, usually read as a stop. In eukaryotes, its co-translational recoding requires the presence of an RNA stem-loop structure, the SECIS element in the 3 untranslated region of (UTR) selenoprotein mRNAs. Despite little sequence conservation, SECIS elements share the same overall secondary structure. Until recently, the lack of a significantly high number of selenoprotein mRNA sequences hampered the identification of other potential sequence conservation. In this work, the web-based tool SECISaln provides for the first time an extensive structure-based sequence alignment of SECIS elements resulting from the well-defined secondary structure of the SECIS RNA and the increased size of the eukaryotic selenoproteome. We have used SECISaln to improve our knowledge of SECIS secondary structure and to discover novel, conserved nucleotide positions and we believe it will be a useful tool for the selenoprotein and RNA scientific communities. AVAILABILITY: SECISaln is freely available as a web-based tool at http://genome.crg.es/software/secisaln/.
机译：摘要：硒蛋白包含第21个氨基酸硒代半胱氨酸，由第一个读码框内的UGA密码子编码，通常被读作终止子。在真核生物中，其共翻译编码需要存在RNA茎环结构，即SEUT元件位于（UTR）硒蛋白mRNA的3个非翻译区域中。尽管几乎不保留序列，但SECIS元素共有相同的整体二级结构。直到最近，缺少大量硒蛋白mRNA序列仍阻碍了其他潜在序列保守性的鉴定。在这项工作中，基于Web的工具SECISaln首次提供了SECIS元素的基于结构的广泛序列比对，这是由于SECIS RNA的明确二级结构和真核硒蛋白组的大小增加所致。我们已经使用SECISaln来提高我们对SECIS二级结构的了解并发现新颖的保守核苷酸位置，并且我们相信它将对硒蛋白和RNA科学界有用。可用性：SECISaln可作为基于Web的工具免费提供，网址为http://genome.crg.es/software/secisaln/。

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