Staden: Analyzing Sequences to Find Genes
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.
KeywordsCodon Usage tRNA Gene Window Length Positional Base Base Frequency Method
- 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
- 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.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
- 6.Fickett, J. W 1982. Recognition of protein coding regions in DNA sequences Nucleic Acids Res. 10, 5303–5318.Google Scholar