Staden: Analyzing Sequences to Find Genes

  • Rodger Staden
Part of the Methods in Molecular Biology book series (MIMB, volume 25)


Three methods are outlined for finding protein genes and one for locating tRNA genes, as are routines for finding open reading frames and displaying the positions of stop codons. All the methods are contained in the program NIP. The correct interpretation of the analyses presented requires a good understanding of the underlying ideas used by the methods. Despite this, this chapter concentrates here on the use of the techniques, the reader is referred to earlier publications (1, 2, 3, 4, 5) for more background information.


Codon Usage tRNA Gene Window Length Positional Base Base Frequency Method 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Staden, R. and McLachlan, A. D. (1982) Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res 10, 151–156.Google Scholar
  2. 2.
    Staden, R (1984) Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes Nucleic Acids Res. 12, 551–567PubMedCrossRefGoogle Scholar
  3. 3.
    Staden, R. (1985) Computer methods to locate genes and signals in nucleic acid sequences, in Genetic Engineering, Principle and Methods, vol. 7 (Setlow, J. K. and Hollaender, A, eds.), Plenum, New York, pp. 67–114.Google Scholar
  4. 4.
    Staden, R. (1990) Fmding Protein Coding Regions in Genomic Sequences, in Methods in Enzymology, vol. 183 (Doolittle, R. F, ed.), Academic, New York, pp. 163–180.Google Scholar
  5. 5.
    Staden, R (1980) A computer program to search for tRNA genes Nucleic Acids Res 8,817–825PubMedCrossRefGoogle Scholar
  6. 6.
    Fickett, J. W 1982. Recognition of protein coding regions in DNA sequences Nucleic Acids Res. 10, 5303–5318.Google Scholar

Copyright information

© Human Press Inc, Totowa, NJ 1994

Authors and Affiliations

  • Rodger Staden
    • 1
  1. 1.MRC Laboratory of Molecular BiologyCambridgeUK

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