Churchill G A, Daniels D L, Waterman M S
Department of Mathematics, University of Southern California, Los Angeles 90089.
Nucleic Acids Res. 1990 Feb 11;18(3):589-97. doi: 10.1093/nar/18.3.589.
A statistical analysis of physical map data for eight restriction enzymes covering nearly the entire genome of E. coli is presented. The methods of analysis are based on a top-down modeling approach which requires no knowledge of the statistical properties of the base sequence. For most enzymes, the distribution of mapped sites is found to be fairly homogeneous. Some heterogeneity in the distribution of sites is observed for the enzymes Pstl and HindIII. In addition, BamHI sites are found to be more evenly dispersed than we would expect for random placement and we speculate on a possible mechanism. A consistent departure from a uniform distribution, observed for each of the eight enzymes, is found to be due to a lack of closely spaced sites. We conclude from our analysis that this departure can be accounted for by deficiencies in the physical map data rather than non-random placement of actual restriction sites. Estimates of the numbers of sites missing from the map are given, based both on the map data itself and on the site frequencies in a sample of sequenced E. coli DNA. We conclude that 5 to 15% of the mapped sites represent multiple sites in the DNA sequence.
本文对覆盖大肠杆菌几乎整个基因组的八种限制酶的物理图谱数据进行了统计分析。分析方法基于一种自上而下的建模方法，该方法不需要了解碱基序列的统计特性。对于大多数酶，发现定位位点的分布相当均匀。对于Pstl和HindIII酶，观察到位点分布存在一些异质性。此外，发现BamHI位点比随机分布时预期的更均匀地分散，我们推测了一种可能的机制。对于这八种酶中的每一种，观察到与均匀分布的一致偏差是由于缺乏紧密间隔的位点。我们从分析中得出结论，这种偏差可以由物理图谱数据中的缺陷来解释，而不是实际限制位点的非随机定位。基于图谱数据本身以及测序的大肠杆菌DNA样本中的位点频率，给出了图谱中缺失位点数量的估计。我们得出结论，5%至15%的定位位点代表DNA序列中的多个位点。
