Hinds P W, Blake R D
Department of Biochemistry, University of Maine, Orono 04469.
J Biomol Struct Dyn. 1985 Dec;3(3):543-9. doi: 10.1080/07391102.1985.10508442.
Codon usage tables have been produced for E. coli, yeast, human, and mouse. The nonrandom employment of codons allows assignment of probability values to trinucleotides in any DNA sequence. These values represent the probability that a given trinucleotide is used as a codon in the organism from which the table is derived. For the graphical delineation of coding areas in DNA sequences, a probability is assigned to each trinucleotide equal to its frequency in the codon table. Averaging and smoothing procedures then greatly enhance the detectability of areas of high average codon probability and better represent the mean codon probability. These manipulations increase graphical clarity without altering the overall magnitude of probabilities. Averaging introduces an error of less than 0.5% between "raw" and smoothed data. This graphical delineation of coding sequences does not depend on the presence of punctuation, ribosomal binding sites, etc: moreover the delineation of introns and exons is also possible.
已经制作了大肠杆菌、酵母、人类和小鼠的密码子使用表。密码子的非随机使用使得能够为任何DNA序列中的三核苷酸分配概率值。这些值代表了给定三核苷酸在推导该表所依据的生物体中用作密码子的概率。为了在DNA序列中以图形方式描绘编码区域，为每个三核苷酸分配一个等于其在密码子表中的频率的概率。然后，平均和平滑程序极大地提高了高平均密码子概率区域的可检测性，并更好地表示平均密码子概率。这些操作增加了图形的清晰度，而不会改变概率的总体大小。平均在“原始”数据和平滑数据之间引入的误差小于0.5%。这种编码序列的图形描绘不依赖于标点符号、核糖体结合位点等的存在；此外，内含子和外显子的描绘也是可能的。
