Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1984 Jan 11;12(1 Pt 1):257–262. doi: 10.1093/nar/12.1part1.257

A convenient method for locating sets of related short sequences in DNA sequences of any length.

A Salemme, A V Furano
PMCID: PMC321002  PMID: 6320091

Abstract

In investigating sequence variants in a family of highly repeated rat DNA, we needed to search the consensus sequence of the repeat unit of this family for short sequences which would become, with one base change, recognition sites for various restriction endonucleases. To do this, we have designed a pair of programs to search DNA sequences of any length for sets of related short sequences, allowing user-specified mismatches in the short sequence. Since putative regulatory regions are generally short sequences, these programs are also useful for locating all possible versions of such sequences in any given DNA. We describe the programs, and present results of searches using the programs.

Full text

PDF
257

Selected References

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

  1. Adams J., Rothman E. D. Estimation of phylogenetic relationships from DNA restriction patterns and selection of endonuclease cleavage sites. Proc Natl Acad Sci U S A. 1982 Jun;79(11):3560–3564. doi: 10.1073/pnas.79.11.3560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brosius J., Dull T. J., Sleeter D. D., Noller H. F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol. 1981 May 15;148(2):107–127. doi: 10.1016/0022-2836(81)90508-8. [DOI] [PubMed] [Google Scholar]
  3. Brutlag D. L., Clayton J., Friedland P., Kedes L. H. SEQ: a nucleotide sequence analysis and recombination system. Nucleic Acids Res. 1982 Jan 11;10(1):279–294. doi: 10.1093/nar/10.1.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hörz W., Zachau H. G. Characterization of distinct segments in mouse satellite DNA by restriction nucleases. Eur J Biochem. 1977 Mar 1;73(2):383–392. doi: 10.1111/j.1432-1033.1977.tb11329.x. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Novotny J. Matrix program to analyze primary structure homology. Nucleic Acids Res. 1982 Jan 11;10(1):127–131. doi: 10.1093/nar/10.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Pech M., Igo-Kemenes T., Zachau H. G. Nucleotide sequence of a highly repetitive component of rat DNA. Nucleic Acids Res. 1979 Sep 25;7(2):417–432. doi: 10.1093/nar/7.2.417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Queen C., Wegman M. N., Korn L. J. Improvements to a program for DNA analysis: a procedure to find homologies among many sequences. Nucleic Acids Res. 1982 Jan 11;10(1):449–456. doi: 10.1093/nar/10.1.449. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  10. Wilbur W. J., Lipman D. J. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. doi: 10.1073/pnas.80.3.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Witney F. R., Furano A. V. The independent evolution of two closely related satellite DNA elements in rats (Rattus). Nucleic Acids Res. 1983 Jan 25;11(2):291–304. doi: 10.1093/nar/11.2.291. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES