Computer analysis of nucleic acid regulatory sequences
- PMID: 270683
- PMCID: PMC431950
- DOI: 10.1073/pnas.74.10.4401
Computer analysis of nucleic acid regulatory sequences
Abstract
We describe a computer program designed to facilitate the analysis of nucleic acid sequences. The program can search several nucleic acid sequences for oligonucleotides common to all of them. It can examine a DNA or RNA sequence for two kinds of homologous regions--repetitions and dyad symmetries. The homologies need not be perfect: mismatches and "looping out" of nucleotides are allowed. The program also finds (A+T)- and (G+C)-rich regions, locates restriction enzyme recognition sites, determines the distribution of di- and trinucleotides, and performs various other functions. We include two representative applications of the program. All published prokaryotic transcription termination sequences (June 1977) were found to share the following features: (i) a string of at least five T residues, (ii) the sequence CGGGC or a close analog immediately preceding the T cluster, (iii) a region of strong dyad symmetry preceding the Ts and including the CGGGC sequence. A sequence of 221 nucleotides consisting of the Escherichia coli trp promoter, operator, and leader was found to contain two strong dyad symmetries. These homologies both occur at known regulatory sites; no comparable homologies occur in regions without regulatory significance.
Similar articles
-
Transcription termination: nucleotide sequence at 3' end of tryptophan operon in Escherichia coli.Proc Natl Acad Sci U S A. 1978 Nov;75(11):5442-6. doi: 10.1073/pnas.75.11.5442. Proc Natl Acad Sci U S A. 1978. PMID: 364481 Free PMC article.
-
A computer algorithm for testing potential prokaryotic terminators.Nucleic Acids Res. 1984 May 25;12(10):4411-27. doi: 10.1093/nar/12.10.4411. Nucleic Acids Res. 1984. PMID: 6374619 Free PMC article.
-
Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro.Nucleic Acids Res. 1981 Feb 11;9(3):563-77. doi: 10.1093/nar/9.3.563. Nucleic Acids Res. 1981. PMID: 7012794 Free PMC article.
-
Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries.Nucleic Acids Res. 1982 Jan 11;10(1):247-63. doi: 10.1093/nar/10.1.247. Nucleic Acids Res. 1982. PMID: 6801626 Free PMC article.
-
Nucleotide sequence of the leader region of the phenylalanine operon of Escherichia coli.Proc Natl Acad Sci U S A. 1978 Sep;75(9):4271-5. doi: 10.1073/pnas.75.9.4271. Proc Natl Acad Sci U S A. 1978. PMID: 360214 Free PMC article.
Cited by
-
Development of a superior strategy for computer-assisted nucleotide sequence analysis.Nucleic Acids Res. 1986 Jan 10;14(1):47-55. doi: 10.1093/nar/14.1.47. Nucleic Acids Res. 1986. PMID: 3753783 Free PMC article.
-
DNA sequence analysis: a procedure to find homologies among many sequences.Nucleic Acids Res. 1986 Jan 10;14(1):543-50. doi: 10.1093/nar/14.1.543. Nucleic Acids Res. 1986. PMID: 3753788 Free PMC article.
-
Significance of similarities in patterns: an application to beta interferon-related DNA on human chromosome 2.Proc Natl Acad Sci U S A. 1985 Jun;82(12):4090-4. doi: 10.1073/pnas.82.12.4090. Proc Natl Acad Sci U S A. 1985. PMID: 3858866 Free PMC article.
-
Nucleotide sequences of trpA of Salmonella typhimurium and Escherichia coli: an evolutionary comparison.Proc Natl Acad Sci U S A. 1979 Oct;76(10):5244-8. doi: 10.1073/pnas.76.10.5244. Proc Natl Acad Sci U S A. 1979. PMID: 388433 Free PMC article.
-
Fine structure of ribosomal RNA. IV. Extraordinary evolutionary conservation in sequences that flank introns in rDNA.Nucleic Acids Res. 1980 Aug 25;8(16):3623-37. doi: 10.1093/nar/8.16.3623. Nucleic Acids Res. 1980. PMID: 6253905 Free PMC article.
References
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
