RNAstructure软件不同版本对FORS-D分析的影响

目的：研究RNAstructure两个不同版本（4．2和3．6版）对FORS-D分析的影响。方法：以HIV-1CRF01_AE基因组为对象，将其分隔成连续的含200碱基的片段，两个连续片段之间互相重叠150碱基。用序列打乱程序将每个片段打乱成10个碱基组成相同的随机片段。用RNAstructure软件分别计算每个片段核酸二级结构的最小自由能。结果：两个不同版本RNAstructure软件获得的FONS、FORS-M和FORS-D值在基因组上具有完全一致的分布。用Z检验分别比较两组数据的平均值，发现4．2版获得的FONS（P〈0．05）和FORS-M（P〈0．01）值明显低于3．6版，而对FORS-D（Z=0．1271，P〉0．05）值没有明显影响。另外，发现GC含量不是两个版本软件造成FONS（P=0．29）和FORS-M（P=0．40）差异的主要因素。结论：使用不同版本的RNAstructure不会影响FORS-D值，但因4．2版可以产生更稳定的二级结构，并具有更高的预测准确性，使用RNAstructure 4．2版进行FORS-D分析将是更好的选择。

Effect of different versions of RNAstructure program on FORS-D analysis

Objective: To investigate the effect of different versions of RNAstructure software on FORS-D analysis.Methods: The genomic sequence of HIV-1 CRF01_AE was selected and divided into successive 200-nucleotide windows.Each overlapped the previous window by 150 nucleotides.The shuffle program was used to generate 10 randomised sequences with same base composition.The minimum free energy of each window was calculated using computer programs: RNA structure version 3.6 and version 4.2, respectively. Results: The completely consistent distribution of FONS,FORS-M and FORS-D values among HIV-1 CRF01_AE genome were obtained by using both versions of RNA structure.The average values of both FONS(Z test: P<0.05) and FORS-M(P<0.01) obtained by version 4.2 software were significantly lower than those of version 3.6 software,respectively.However,there was no significant difference in FORS-D values(Z=0.1271,P>0.05) between the two versions.Furthermore,we demonstrated that the differences in FONS(P=0.29) and FORS-M(P=0.40) values caused by different RNAstructure versions were not associated with GC%. Conclusion: These results suggested that the application of different RNAstructure versions doesn't influence the FORS-D analysis,and that RNAstructure version 4.2 is more suitable for FORS-D analysis than RNAstructure version 3.6 because of its higher accuracy in prediction of secondary structure.