Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Apr 11;11(7):2221–2231. doi: 10.1093/nar/11.7.2221

Regulatory pattern identification in nucleic acid sequences

JR Sadler 1, MS Waterman 2, TF Smith 3
PMCID: PMC325874  PMID: 6340068

Abstract

In addition to the sequence homologies and statistical patterns identified among numerous genetic sequences, there are subtler classes of patterns for which most current computer search methods offer very limited utility. This class includes various presumptive eukaryotic regulatory sites. A critique of the often employed consensus and local homology methods suggests the need for new tools. In particular, such new methods should use the positional and structural data now becoming available on exactly what it is that is recognized in the DNA sequence by sequence-specific binding proteins.

Full text

PDF
2221

Selected References

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

  1. Breathnach R., Benoist C., O'Hare K., Gannon F., Chambon P. Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4853–4857. doi: 10.1073/pnas.75.10.4853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Darnell J. E., Jr Variety in the level of gene control in eukaryotic cells. Nature. 1982 Jun 3;297(5865):365–371. doi: 10.1038/297365a0. [DOI] [PubMed] [Google Scholar]
  3. Dickerson R. E., Drew H. R., Conner B. N., Wing R. M., Fratini A. V., Kopka M. L. The anatomy of A-, B-, and Z-DNA. Science. 1982 Apr 30;216(4545):475–485. doi: 10.1126/science.7071593. [DOI] [PubMed] [Google Scholar]
  4. Dickerson R. E., Drew H. R. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J Mol Biol. 1981 Jul 15;149(4):761–786. doi: 10.1016/0022-2836(81)90357-0. [DOI] [PubMed] [Google Scholar]
  5. Efstratiadis A., Posakony J. W., Maniatis T., Lawn R. M., O'Connell C., Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M., Slightom J. L. The structure and evolution of the human beta-globin gene family. Cell. 1980 Oct;21(3):653–668. doi: 10.1016/0092-8674(80)90429-8. [DOI] [PubMed] [Google Scholar]
  6. Hentschel C. C., Birnstiel M. L. The organization and expression of histone gene families. Cell. 1981 Aug;25(2):301–313. doi: 10.1016/0092-8674(81)90048-9. [DOI] [PubMed] [Google Scholar]
  7. Lerner M. R., Boyle J. A., Mount S. M., Wolin S. L., Steitz J. A. Are snRNPs involved in splicing? Nature. 1980 Jan 10;283(5743):220–224. doi: 10.1038/283220a0. [DOI] [PubMed] [Google Scholar]
  8. McKnight S. L., Kingsbury R. Transcriptional control signals of a eukaryotic protein-coding gene. Science. 1982 Jul 23;217(4557):316–324. doi: 10.1126/science.6283634. [DOI] [PubMed] [Google Scholar]
  9. Moreau J., Marcaud L., Maschat F., Kejzlarova-Lepesant J., Lepesant J. A., Scherrer K. A + T-rich linkers define functional domains in eukaryotic DNA. Nature. 1982 Jan 21;295(5846):260–262. doi: 10.1038/295260a0. [DOI] [PubMed] [Google Scholar]
  10. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
  11. Ohlendorf D. H., Anderson W. F., Fisher R. G., Takeda Y., Matthews B. W. The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature. 1982 Aug 19;298(5876):718–723. doi: 10.1038/298718a0. [DOI] [PubMed] [Google Scholar]
  12. Pabo C. O., Krovatin W., Jeffrey A., Sauer R. T. The N-terminal arms of lambda repressor wrap around the operator DNA. Nature. 1982 Jul 29;298(5873):441–443. doi: 10.1038/298441a0. [DOI] [PubMed] [Google Scholar]
  13. Pabo C. O., Lewis M. The operator-binding domain of lambda repressor: structure and DNA recognition. Nature. 1982 Jul 29;298(5873):443–447. doi: 10.1038/298443a0. [DOI] [PubMed] [Google Scholar]
  14. Patel D. J., Pardi A., Itakura K. DNA conformation, dynamics, and interactions in solution. Science. 1982 May 7;216(4546):581–590. doi: 10.1126/science.6280281. [DOI] [PubMed] [Google Scholar]
  15. Proudfoot N. J., Brownlee G. G. 3' non-coding region sequences in eukaryotic messenger RNA. Nature. 1976 Sep 16;263(5574):211–214. doi: 10.1038/263211a0. [DOI] [PubMed] [Google Scholar]
  16. Proudfoot N. J., Shander M. H., Manley J. L., Gefter M. L., Maniatis T. Structure and in vitro transcription of human globin genes. Science. 1980 Sep 19;209(4463):1329–1336. doi: 10.1126/science.6158093. [DOI] [PubMed] [Google Scholar]
  17. Sauer R. T., Yocum R. R., Doolittle R. F., Lewis M., Pabo C. O. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature. 1982 Jul 29;298(5873):447–451. doi: 10.1038/298447a0. [DOI] [PubMed] [Google Scholar]
  18. Schmid C. W., Jelinek W. R. The Alu family of dispersed repetitive sequences. Science. 1982 Jun 4;216(4550):1065–1070. doi: 10.1126/science.6281889. [DOI] [PubMed] [Google Scholar]
  19. Smith T. F., Sadler J. R. The nature of lactose operator constitive mutations. J Mol Biol. 1971 Jul 28;59(2):273–305. doi: 10.1016/0022-2836(71)90051-9. [DOI] [PubMed] [Google Scholar]
  20. Smith T. F., Waterman M. S., Fitch W. M. Comparative biosequence metrics. J Mol Evol. 1981;18(1):38–46. doi: 10.1007/BF01733210. [DOI] [PubMed] [Google Scholar]
  21. Smith T. F., Waterman M. S. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195–197. doi: 10.1016/0022-2836(81)90087-5. [DOI] [PubMed] [Google Scholar]

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

RESOURCES