MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a key role in gene regulation in both plants and animals. MicroRNA biogenesis involves the enzymatic processing of a primary RNA transcript. The final step is the production of a duplex molecule, often designated as miRNA:miRNA*, that will yield a functional miRNA by separation of the two strands. This miRNA will be incorporated into the RNA-induced silencing complex, which subsequently will bind to its target mRNA in order to suppress its expression. The analysis of miRNAs is still a developing area for computational biology with many open questions regarding the structure and function of this important class of molecules. Here, we present StarSeeker, a simple tool that outputs the putative miRNA* sequence given the precursor and the mature sequences. We evaluated StarSeeker using a dataset consisting of all plant sequences available in miRBase (6992 precursor sequences and 8496 mature sequences). The program returned a total of 15,468 predicted miRNA* sequences. Of these, 2650 sequences were matched to annotated miRNAs (~ 90% of the miRBase-annotated sequences). The remaining predictions could not be verified, mainly because they do not comply with the rule requiring the two overhanging nucleotides in the duplex molecule. The expression pattern of some miRNAs in plants can be altered under various abiotic stress conditions. Potential miRNA* molecules that do not degrade can thus be detected and also discovered in high-throughput sequencing data, helping us to understand their role in gene regulation.

中文翻译：

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StarSeeker：基于前体分子的二级结构建模的成熟双链microRNA序列识别自动化工具

微小RNA（miRNA）是小的非编码RNA分子，在动植物的基因调控中起着关键作用。MicroRNA生物发生涉及初级RNA转录物的酶促加工。最后一步是通常称为miRNA：miRNA *的双链体分子的产生，该分子将通过两条链的分离产生功能性miRNA。将该miRNA掺入RNA诱导的沉默复合物中，随后将其结合至其靶mRNA，以抑制其表达。miRNA的分析仍是计算生物学的发展领域，关于这一重要分子类别的结构和功能存在许多悬而未决的问题。在这里，我们介绍StarSeeker，这是一个简单的工具，可以根据给定的前体和成熟序列输出假定的miRNA *序列。我们使用由miRBase中可用的所有植物序列（6992个前体序列和8496个成熟序列）组成的数据集评估了StarSeeker。该程序总共返回了15468个预测的miRNA *序列。其中，有2650个序列与带注释的miRNA相匹配（约占miRBase注释序列的90％）。其余的预测无法得到验证，主要是因为它们不符合要求双链体分子中两个突出的核苷酸的规则。在各种非生物胁迫条件下，一些miRNA在植物中的表达方式可以改变。因此，可以检测出不降解的潜在miRNA *分子，并在高通量测序数据中发现它们，从而帮助我们了解它们在基因调控中的作用。