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. 1984 Jan 11;12(1 Pt 2):505–519. doi: 10.1093/nar/12.1part2.505

Computer methods to locate signals in nucleic acid sequences.

R Staden
PMCID: PMC321067  PMID: 6364039

Abstract

This paper describes computer methods for locating signals in nucleic acid sequences. The signals include ribosome binding sites, promoter sequences and splice junctions. The methods are of use both to those trying to interpret the function of newly determined sequences and to those studying the molecular mechanisms involved in the recognition of these special signal sequences.

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Selected References

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

  1. An G., Friesen J. D. Characterization of promoter-cloning plasmids: analysis of operon structure in the rif region of Escherichia coli and isolation of an enhanced internal promoter mutant. J Bacteriol. 1980 Dec;144(3):904–916. doi: 10.1128/jb.144.3.904-916.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Berman M. L., Landy A. Promoter mutations in the transfer RNA gene tyrT of Escherichia coli. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4303–4307. doi: 10.1073/pnas.76.9.4303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Calos M. P. DNA sequence for a low-level promoter of the lac repressor gene and an 'up' promoter mutation. Nature. 1978 Aug 24;274(5673):762–765. doi: 10.1038/274762a0. [DOI] [PubMed] [Google Scholar]
  4. Duester G., Campen R. K., Holmes W. M. Nucleotide sequence of an Escherichia coli tRNA (Leu 1) operon and identification of the transcription promoter signal. Nucleic Acids Res. 1981 May 11;9(9):2121–2139. doi: 10.1093/nar/9.9.2121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Gilbert S. F., de Boer H. A., Nomura M. Identification of initiation sites for the in vitro transcription of rRNA operons rrnE and rrnA in E. coli. Cell. 1979 May;17(1):211–224. doi: 10.1016/0092-8674(79)90309-x. [DOI] [PubMed] [Google Scholar]
  6. Gold L., Pribnow D., Schneider T., Shinedling S., Singer B. S., Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. doi: 10.1146/annurev.mi.35.100181.002053. [DOI] [PubMed] [Google Scholar]
  7. Harr R., Häggström M., Gustafsson P. Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res. 1983 May 11;11(9):2943–2957. doi: 10.1093/nar/11.9.2943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Heilig R., Perrin F., Gannon F., Mandel J. L., Chambon P. The ovalbumin gene family: structure of the X gene and evolution of duplicated split genes. Cell. 1980 Jul;20(3):625–637. doi: 10.1016/0092-8674(80)90309-8. [DOI] [PubMed] [Google Scholar]
  10. Horii T., Ogawa T., Ogawa H. Organization of the recA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):313–317. doi: 10.1073/pnas.77.1.313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Jaurin B., Grundström T., Edlund T., Normark S. The E. coli beta-lactamase attenuator mediates growth rate-dependent regulation. Nature. 1981 Mar 19;290(5803):221–225. doi: 10.1038/290221a0. [DOI] [PubMed] [Google Scholar]
  12. Lawn R. M., Efstratiadis A., O'Connell C., Maniatis T. The nucleotide sequence of the human beta-globin gene. Cell. 1980 Oct;21(3):647–651. doi: 10.1016/0092-8674(80)90428-6. [DOI] [PubMed] [Google Scholar]
  13. MacLeod A. R., Karn J., Brenner S. Molecular analysis of the unc-54 myosin heavy-chain gene of Caenorhabditis elegans. Nature. 1981 Jun 4;291(5814):386–390. doi: 10.1038/291386a0. [DOI] [PubMed] [Google Scholar]
  14. Mandecki W., Reznikoff W. S. A lac promoter with a changed distance between -10 and -35 regions. Nucleic Acids Res. 1982 Feb 11;10(3):903–912. doi: 10.1093/nar/10.3.903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Mount S. M. A catalogue of splice junction sequences. Nucleic Acids Res. 1982 Jan 22;10(2):459–472. doi: 10.1093/nar/10.2.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Post L. E., Strycharz G. D., Nomura M., Lewis H., Dennis P. P. Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1697–1701. doi: 10.1073/pnas.76.4.1697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Pribnow D. Bacteriophage T7 early promoters: nucleotide sequences of two RNA polymerase binding sites. J Mol Biol. 1975 Dec 15;99(3):419–443. doi: 10.1016/s0022-2836(75)80136-7. [DOI] [PubMed] [Google Scholar]
  18. Rosenberg M., Court D., Shimatake H., Brady C., Wulff D. L. The relationship between function and DNA sequence in an intercistronic regulatory region in phage lambda. Nature. 1978 Mar 30;272(5652):414–423. doi: 10.1038/272414a0. [DOI] [PubMed] [Google Scholar]
  19. Sancar A., Stachelek C., Konigsberg W., Rupp W. D. Sequences of the recA gene and protein. Proc Natl Acad Sci U S A. 1980 May;77(5):2611–2615. doi: 10.1073/pnas.77.5.2611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sargan D. R., Gregory S. P., Butterworth P. H. A possible novel interaction between the 3'-end of 18 S ribosomal RNA and the 5'-leader sequence of many eukaryotic messenger RNAs. FEBS Lett. 1982 Oct 18;147(2):133–136. doi: 10.1016/0014-5793(82)81026-0. [DOI] [PubMed] [Google Scholar]
  21. Schaller H., Gray C., Herrmann K. Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd. Proc Natl Acad Sci U S A. 1975 Feb;72(2):737–741. doi: 10.1073/pnas.72.2.737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Schmeissner U., Court D., Shimatake H., Rosenberg M. Promoter for the establishment of repressor synthesis in bacteriophage lambda. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3191–3195. doi: 10.1073/pnas.77.6.3191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Seeburg P. H., Nüsslein C., Schaller H. Interaction of RNA polymerase with promoters from bacteriophage fd. Eur J Biochem. 1977 Mar 15;74(1):107–113. doi: 10.1111/j.1432-1033.1977.tb11372.x. [DOI] [PubMed] [Google Scholar]
  24. Steege D. A. 5'-Terminal nucleotide sequence of Escherichia coli lactose repressor mRNA: features of translational initiation and reinitiation sites. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4163–4167. doi: 10.1073/pnas.74.10.4163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Stefano J. E., Gralla J. D. Spacer mutations in the lac ps promoter. Proc Natl Acad Sci U S A. 1982 Feb;79(4):1069–1072. doi: 10.1073/pnas.79.4.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Stormo G. D., Schneider T. D., Gold L., Ehrenfeucht A. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res. 1982 May 11;10(9):2997–3011. doi: 10.1093/nar/10.9.2997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Takanami M., Sugimoto K., Sugisaki H., Okamoto T. Sequence of promoter for coat protein gene of bacteriophage fd. Nature. 1976 Mar 25;260(5549):297–302. doi: 10.1038/260297a0. [DOI] [PubMed] [Google Scholar]
  28. Woo S. L., Beattie W. G., Catterall J. F., Dugaiczyk A., Staden R., Brownlee G. G., O'Malley B. W. Complete nucleotide sequence of the chicken chromosomal ovalbumin gene and its biological significance. Biochemistry. 1981 Oct 27;20(22):6437–6446. doi: 10.1021/bi00525a024. [DOI] [PubMed] [Google Scholar]
  29. Youderian P., Bouvier S., Susskind M. M. Sequence determinants of promoter activity. Cell. 1982 Oct;30(3):843–853. doi: 10.1016/0092-8674(82)90289-6. [DOI] [PubMed] [Google Scholar]
  30. de Boer H. A., Gilbert S. F., Nomura M. DNA sequences of promoter regions for rRNA operons rrnE and rrnA in E. coli. Cell. 1979 May;17(1):201–209. doi: 10.1016/0092-8674(79)90308-8. [DOI] [PubMed] [Google Scholar]

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