Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1991 Aug 11;19(15):4241–4246. doi: 10.1093/nar/19.15.4241

Assessment of inhomogeneities in an E. coli physical map.

S Karlin 1, C Macken 1
PMCID: PMC328568  PMID: 1870978

Abstract

A statistical method based on r-fragments, sums of distances between (r + 1) consecutive restriction enzyme sites, is introduced for detecting nonrandomness in the distribution or too markers in sequence data. The technique is applicable whenever large numbers of markers are available and will detect clumping, excessive dispersion or too much evenness of spacing of the markers. It is particularly adapted to varying the scale on which inhomogeneities can be detected, from nearest neighbor interactions to more distant interactions. The r-fragment procedure is applied primarily to the Kohara et al. (1) physical map of E. coli. Other applications to DAM methylation sites in E. coli and NotI sites in human chromosome 21 are presented. Restriction sites for the eight enzymes used in (1) appear to be randomly distributed, although at widely differing densities. These conclusions are substantially in agreement with the analysis of Churchill et al. (3). Extreme variability in the density of the eight restriction enzyme sites cannot be explained by variability in mono-, di- or trinucleotide frequencies.

Full text

PDF
4241

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bernardi G., Mouchiroud D., Gautier C., Bernardi G. Compositional patterns in vertebrate genomes: conservation and change in evolution. J Mol Evol. 1988 Dec;28(1-2):7–18. doi: 10.1007/BF02143493. [DOI] [PubMed] [Google Scholar]
  2. Bird A. P. CpG-rich islands and the function of DNA methylation. Nature. 1986 May 15;321(6067):209–213. doi: 10.1038/321209a0. [DOI] [PubMed] [Google Scholar]
  3. Brendel V., Beckmann J. S., Trifonov E. N. Linguistics of nucleotide sequences: morphology and comparison of vocabularies. J Biomol Struct Dyn. 1986 Aug;4(1):11–21. doi: 10.1080/07391102.1986.10507643. [DOI] [PubMed] [Google Scholar]
  4. Churchill G. A., Daniels D. L., Waterman M. S. The distribution of restriction enzyme sites in Escherichia coli. Nucleic Acids Res. 1990 Feb 11;18(3):589–597. doi: 10.1093/nar/18.3.589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Gilson E., Saurin W., Perrin D., Bachellier S., Hofnung M. Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 1991 Apr 11;19(7):1375–1383. doi: 10.1093/nar/19.7.1375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Jukes T. H., Bhushan V. Silent nucleotide substitutions and G + C content of some mitochondrial and bacterial genes. J Mol Evol. 1986;24(1-2):39–44. doi: 10.1007/BF02099949. [DOI] [PubMed] [Google Scholar]
  7. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  8. Krawiec S., Riley M. Organization of the bacterial chromosome. Microbiol Rev. 1990 Dec;54(4):502–539. doi: 10.1128/mr.54.4.502-539.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. McClelland M., Jones R., Patel Y., Nelson M. Restriction endonucleases for pulsed field mapping of bacterial genomes. Nucleic Acids Res. 1987 Aug 11;15(15):5985–6005. doi: 10.1093/nar/15.15.5985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Nussinov R. Strong doublet preferences in nucleotide sequences and DNA geometry. J Mol Evol. 1984;20(2):111–119. doi: 10.1007/BF02257371. [DOI] [PubMed] [Google Scholar]
  11. Rudd K. E., Miller W., Ostell J., Benson D. A. Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map. Nucleic Acids Res. 1990 Jan 25;18(2):313–321. doi: 10.1093/nar/18.2.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Rudd K. E., Miller W., Werner C., Ostell J., Tolstoshev C., Satterfield S. G. Mapping sequenced E.coli genes by computer: software, strategies and examples. Nucleic Acids Res. 1991 Feb 11;19(3):637–647. doi: 10.1093/nar/19.3.637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Stückle E. E., Emmrich C., Grob U., Nielsen P. J. Statistical analysis of nucleotide sequences. Nucleic Acids Res. 1990 Nov 25;18(22):6641–6647. doi: 10.1093/nar/18.22.6641. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES