A comparison of RNA folding measures.
A comparison of RNA folding measures.
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DOI：
10.1186/1471-2105-6-241
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发表时间：
2005-10-03
影响因子：
3
通讯作者：
Moulton V
中科院分区：
文献类型：
--
作者：
Freyhult E;Gardner PP;Moulton V
在过去的几十年里，关于非编码 RNA 序列 (ncRNA) 是否以比随机序列更明确的方式折叠的问题进行了大量讨论。在本文中，我们研究了几种现有的 RNA 序列折叠程度的测量方法，并比较了这些测量方法在大范围 Rfam ncRNA 家族中的行为。此类测量可用于识别新的 ncRNA，并指示替代 RNA 折叠的存在。我们的分析表明，ncRNA（而非 mRNA）通常比具有相同二核苷酸频率的随机序列具有更低的最小自由能 (MFE)。此外，即使 MFE 很大，许多 ncRNA 似乎也没有独特的折叠，而是有几个替代的折叠，至少在计算机中折叠时是这样。此外，我们发现六项调查指标存在不同程度的相关性。由于不同测量之间的相关性，我们发现在 RNA 折叠研究中仅使用其中两个就足够了，一个用于测试所讨论的序列是否比具有相同二核苷酸频率（Z 分数）的随机序列具有更低的能量，另一个用于查看该序列是否具有独特的折叠（平均碱基对距离，D）。
In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees. Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score) and the other to see if the sequence has a unique fold (the average base-pair distance, D).
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