FORS-D分析软件“Random_fold_scan”和不同碱基随机打乱算法对FORS-D分析的影响  

A FORS-D analysis software "Random_fold_scan" and the influence of different shuffle approaches on FORS-D analysis

作　　者：徐顺高[1] 魏继福[2] 张驰宇[1] 

机构地区：[1]江苏大学医学技术学院,江苏镇江212013 [2]南京医科大学第一附属医院临床试验研究中心,江苏南京210029

出　　处：《江苏大学学报（医学版）》2007年第6期461-466,470,共7页Journal of Jiangsu University：Medicine Edition

基　　金：国家自然科学基金资助项目(30600352);江苏省自然科学基金-创新人才启动项目(BK2006550);江苏大学高级人才启动项目(2281270002)

摘　　要：目的:开发FORS-D分析软件,并比较不同碱基随机打乱算法对FORS-D分析的影响。方法:根据单、双、三碱基及密码子随机打乱算法,用ActivePerl-5.8.8.820编写"Random_fold_scan"软件,它通过系统命令调用RNA-structure4.2来计算FORS-D值。用4种碱基随机打乱算法分别计算来自不同物种的12个mRNA序列,并且比较它们对FORS-D值的影响。结果:4种随机打乱策略不影响核酸序列的FORS-D分布趋势,但是单碱基打乱算法可以获得比其他3种算法更低的FORS-D值。比较4种打乱算法获得的FORS-D值的Z-score分布,发现单碱基打乱产生的FORS-D值显著小于0的比例最高,相反,FORS-D值显著大于0的比例最低。结论:单碱基随机打乱算法能够彻底破坏原始核酸的序列信息,在概念和理论上能够真正反映FORS-D的生物学涵义。这表明FORS-D分析中单碱基打乱足以给出准确、可靠的数据信息。此外,我们开发了软件"Random_fold_scan"用于FORS-D分析。Objective： To develop FORS-D analysis software and to investigate the influence of four shuffle approaches on FORS-D analysis. Methods： Based on mononucleotide, dinucleotide, trinucleotide and codon shuffling approaches, FORS-D analysis software “Random_fold_scan” was written in ActivePerl- 5.8.8. 820. The software “RNAstructure4.2” was implemented in our software for calculating the minimum free energy of natural sequence. The FORS-D analysis of 12 mRNAs from different species was performed using the four shuffling approaches of our software. Results： The usages of four shuffling approaches do not influence the distributions of FORS-D values of 12 mRNAs. The comparison between the four shuffling approaches showed that mononucleotide shuffling resulted in lower FORS-D values than the others. Further- more, according to the distribution of Z-Score, we found that mononucleotide shuffling resulted in higher percentage of FORS-D values significantly less than zero than other shuffling approaches. Contrarily, the percentage of FORS-D values significantly more than zero appeared to be lower when mononucleotide shuffling was used. Conclusion： Mononucleotide shuffling can disrupt absolutely the base order of natural sequence, which reflects and interprets the biological meaning of FORS-D in conceptual and theoretic aspects. It suggests that the usage of mononucleotide shuffling is optimal for FORS-D analysis. Furthermore, we developed software “Random_fold_scan” for FORS-D analysis.

关 键 词：FORS-D分析 Z-SCORE 单碱基随机打乱 双碱基随机打乱 

分 类 号：R318.04[医药卫生—生物医学工程]