Doran Jonathon, Strauss William M
Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Colorado 80309, USA.
DNA Cell Biol. 2007 May;26(5):353-60. doi: 10.1089/dna.2006.0546.
MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate mRNAs through a sequence-specific mechanism. By virtue of their structure and mechanism of action, computational methods have been devised to investigate the encoding of miRNA genes and the targets of miRNA action. A variety of assumptions have predicated the implementation of these various computational solutions. Evolutionary sequence conservation, secondary structure, and folding energetics are some of the assumptions that have been used. The success of these different computational solutions has been evaluated for both elucidation of new miRNAs and deducing targets of miRNA action. While the focus is on search techniques for new miRNAs, we have compared the programs miRseeker, miRScan, PalGrade, ProMiR, and miRAlign as examples of implementation of these techniques. For these programs, a benchmark comparison between theoretical estimation and actual identification is possible. We have also compared the target prediction programs TargetScanS, PicTar, DIANA-microT, miRanda, and RNAhybrid. However, it is difficult to rigorously assess the benchmark performance of these programs due to the difficulty in confirming their theoretical predictions.
微小RNA（miRNA）是一类小的非编码RNA分子，它们通过序列特异性机制调控信使核糖核酸（mRNA）。基于其结构和作用机制，人们设计了计算方法来研究miRNA基因的编码以及miRNA作用的靶标。多种假设为这些不同的计算解决方案的实施提供了依据。进化序列保守性、二级结构和折叠能量学是其中一些被采用的假设。这些不同计算解决方案在阐明新的miRNA和推断miRNA作用靶标方面的成功已经得到评估。虽然重点是寻找新miRNA的搜索技术，但我们以miRseeker、miRScan、PalGrade、ProMiR和miRAlign这些程序为例，比较了这些技术的实施情况。对于这些程序，可以在理论估计和实际识别之间进行基准比较。我们还比较了靶标预测程序TargetScanS、PicTar、DIANA-microT、miRanda和RNAhybrid。然而，由于难以证实其理论预测，很难严格评估这些程序的基准性能。
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