A Convenient Method for Locating Sets of Related Short Sequences in DNA Sequences of Any Length

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1984 Jan 11

PMID 6320091

Authors

A Salemme

A V Furano

Affiliations

Soon will be listed here.

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.

References

Adams J, Rothman E . Estimation of phylogenetic relationships from DNA restriction patterns and selection of endonuclease cleavage sites. Proc Natl Acad Sci U S A. 1982; 79(11):3560-4. PMC: 346461. DOI: 10.1073/pnas.79.11.3560. View

Witney F, Furano A . The independent evolution of two closely related satellite DNA elements in rats (Rattus). Nucleic Acids Res. 1983; 11(2):291-304. PMC: 325715. DOI: 10.1093/nar/11.2.291. View

Wilbur W, Lipman D . Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983; 80(3):726-30. PMC: 393452. DOI: 10.1073/pnas.80.3.726. View

NEEDLEMAN S, Wunsch C . A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48(3):443-53. DOI: 10.1016/0022-2836(70)90057-4. View

Horz W, Zachau H . Characterization of distinct segments in mouse satellite DNA by restriction nucleases. Eur J Biochem. 1977; 73(2):383-92. DOI: 10.1111/j.1432-1033.1977.tb11329.x. View

Queen C, Wegman M, Korn L . Improvements to a program for DNA analysis: a procedure to find homologies among many sequences. Nucleic Acids Res. 1982; 10(1):449-56. PMC: 326145. DOI: 10.1093/nar/10.1.449. View

Rosenberg M, Court D . Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979; 13:319-53. DOI: 10.1146/annurev.ge.13.120179.001535. View

Brosius J, Dull T, Sleeter D, Noller H . Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol. 1981; 148(2):107-27. DOI: 10.1016/0022-2836(81)90508-8. View

Novotny J . Matrix program to analyze primary structure homology. Nucleic Acids Res. 1982; 10(1):127-31. PMC: 326120. DOI: 10.1093/nar/10.1.127. View

10.

Brutlag D, Clayton J, Friedland P, Kedes L . SEQ: a nucleotide sequence analysis and recombination system. Nucleic Acids Res. 1982; 10(1):279-94. PMC: 326133. DOI: 10.1093/nar/10.1.279. View

11.

Pech M, Zachau H . Nucleotide sequence of a highly repetitive component of rat DNA. Nucleic Acids Res. 1979; 7(2):417-32. PMC: 328026. DOI: 10.1093/nar/7.2.417. View