Galat A, Goldberg I H
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.
Comput Appl Biosci. 1987 Nov;3(4):333-8. doi: 10.1093/bioinformatics/3.4.333.
Computer-aided analysis of autoradiographic films of DNA fragments is presented. The Powell least-squares procedure is used for optimization of parameters for components of complex densitometric curves. Since each densitometric spectrum may be divided for several non-overlapped blocks of bands, there is no upper limit on the number of parameters which must be optimized. Eight shapes for the component bands are utilized: symmetric and asymmetric Gauss and Cauchy functions, direct, symmetric and asymmetric product of Gauss function and inverse of Cauchy function, and log-normal function. The probability of DNA cleavage is calculated with correction for multiple cuts. The methods presented was applied to detailed analysis of densitometric spectra of a 21-bp DNA restriction fragment and allowed for direct correlation between structural microheterogeneity of DNA and the resulting cutting pattern. This method should facilitate the analysis of densitometric data from antibiotic-induced cleavage of DNA and footprinting experiments.
本文介绍了对DNA片段放射自显影片的计算机辅助分析。采用鲍威尔最小二乘法来优化复杂光密度曲线各成分的参数。由于每个光密度谱可划分为几个不重叠的条带块，因此必须优化的参数数量没有上限。使用了八种成分条带形状：对称和不对称高斯函数、柯西函数、高斯函数与柯西函数倒数的直接、对称和不对称乘积，以及对数正态函数。计算DNA切割概率时会对多次切割进行校正。所提出的方法应用于对一个21碱基对DNA限制片段光密度谱的详细分析，并能够直接关联DNA的结构微异质性与所得切割模式。该方法应有助于分析来自抗生素诱导的DNA切割和足迹实验的光密度数据。
