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Nucleic Acids Res. Jan 11, 1982; 10(1): 141–156.
PMCID: PMC326122

Codon preference and its use in identifying protein coding regions in long DNA sequences

Abstract

This paper describes a computer method that uses codon preference to help find protein coding regions in long DNA sequences. The method can distinguish between introns and exons and can help to detect sequencing errors.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Staden R. A computer program to search for tRNA genes. Nucleic Acids Res. 1980 Feb 25;8(4):817–825. [PMC free article] [PubMed]
  • Godson GN, Barrell BG, Staden R, Fiddes JC. Nucleotide sequence of bacteriophage G4 DNA. Nature. 1978 Nov 16;276(5685):236–247. [PubMed]
  • Grantham R, Gautier C, Gouy M, Mercier R, Pavé A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980 Jan 11;8(1):r49–r62. [PMC free article] [PubMed]
  • MacLeod AR, 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. [PubMed]
  • Nussinov R. Some rules in the ordering of nucleotides in the DNA. Nucleic Acids Res. 1980 Oct 10;8(19):4545–4562. [PMC free article] [PubMed]
  • Godson GN, Barrell BG, Staden R, Fiddes JC. Nucleotide sequence of bacteriophage G4 DNA. Nature. 1978 Nov 16;276(5685):236–247. [PubMed]
  • Beck E, Sommer R, Auerswald EA, Kurz C, Zink B, Osterburg G, Schaller H, Sugimoto K, Sugisaki H, Okamoto T, et al. Nucleotide sequence of bacteriophage fd DNA. Nucleic Acids Res. 1978 Dec;5(12):4495–4503. [PMC free article] [PubMed]
  • Gay NJ, Walker JE. The atp operon: nucleotide sequence of the promoter and the genes for the membrane proteins, and the delta subunit of Escherichia coli ATP-synthase. Nucleic Acids Res. 1981 Aug 25;9(16):3919–3926. [PMC free article] [PubMed]
  • Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. [PubMed]
  • Wain-Hobson S, Nussinov R, Brown RJ, Sussman JL. Preferential codon usage in genes. Gene. 1981 May;13(4):355–364. [PubMed]
  • Shepherd JC. Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1596–1600. [PMC free article] [PubMed]
  • Shulman MJ, Steinberg CM, Westmoreland N. The coding function of nucleotide sequences can be discerned by statistical analysis. J Theor Biol. 1981 Feb 7;88(3):409–420. [PubMed]

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