codon usage

[Keith Robison]

There have been a number of questions here on the use of codon frequency
information to predict coding regions.  Here are some references:

Bulmer, M.  1987.  Nature 325:728-730.

Bulmer, M.  1988.  J.Theor.Biol 133:67-71

Fickett, JW.  1982.  Nuc.Acids.Res 10:5303-5318.
	Recognition of protein coding regions in DNA sequences

Gribskov, M, J Devereux, and RR Burgess.  1984.  Nuc.Acids.Res 12:539-549.
	The codon preference plot: graphic analysis of protein coding  
	sequences and prediction of gene expression.

Li, W-H.  1987.  J.Mol.Evol. 24:337-345.

McLachlan, AD. et al  1984  Nuc.Acids.Res 12:9567-9575.

Ohno, S  1988.  PNAS 85:4378-4382.
	Codon preference is but an illusion created by the construction 
	principle of coding sequences.

Sharp, PM and M. Bulmer.  1988.  Gene 63:141-145.
	Selective differences among translation termination codons.
		
Sharp, PM and W-H Li.  1986.  J.Mol.Evol. 24:28-38.
		
Sharp, PM and W-H Li.  1987.  Nuc.Acids.Res 15:1281-1295.
		
Sharp, PM et al.  1986.  Nuc.Acids.Res 14:5125-5139.

Staden, R.  1984.  Nuc.Acids.Res 12:505-519
	Computer methods to locate signals in nucleic acid sequences
		
Staden, R.  1984.  Nuc.Acids.Res 12:521-538
	Graphic methods to determine the function of nucleic acid sequences
		
Staden, R.  1984.  Nuc.Acids.Res 12:551-567
	Measurements of the effects that coding for a protein has on a DNA 
	sequence and their use for finding genes.




Keith Robison
Harvard University
Program in Biochemistry, Molecular, Cellular, and Developmental Biology

robison at ribo.harvard.edu