摘要
目的寻找最优的DNA解链温度(Tm)预测方法。方法使用12种Tm值预测方法计算来自文献中348个实测数据的Tm值,将每种方法预测值与实验标准值的差值进行四分位法作图,并计算各方法残差平方和的自然对数,排序后比较12种预测方法的优劣。结果使用最邻近法并结合SantaLucia 1998热力学参数表和Schildkraut1965盐浓度校正公式所预测的Tm值最接近实测数据。结论最邻近法是最准确的Tm值预测方法,而且当PCR引物的GC含量越接近于50%时,其预测准确率越高。
Objective To find the optimal method for predicting the melting temperature（Tm） of DNA.Methods The Tm value of 348 experiment-derived data from literature was calculated by the 12 Tm prediction methods.The interquartile figure was drawn to show the difference between the predicted Tm values and the experimental benchmark data set,before the natural logarithm of the sum of square（SSQ） was compared between each prediction method and experiment-derived data.Results Our data indicated that the SSQ value obtained by using the ＂Nearest Neighbor＂（NN） model in combination with the thermodynamics table of ＂SantaLucia 1998＂ and the salt correction formula of ＂Schildkraut 1965＂ was the minimum one among the 12 Tm prediction methods.Conclusion The NN model is the most accurate and robust method for Tm prediction,especially for the primers with a GC content close to 50%.
出处
《军事医学》
CAS
CSCD
北大核心
2011年第3期231-235,共5页
Military Medical Sciences
基金
国家科技重大专项资助项目(2009ZX09503-002,2009ZX09301-002,2009ZX09103-616)
国家自然科学基金资助项目(30900862,30900830,30800196)
蛋白质组学国家重点实验室课题(SKLP-K201004,SKLP-O201002)
关键词
解链温度
最邻近法
引物
探针
热力学
melting temperature
Nearest Neighbor
primer
probe
thermodynamics
