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Nucleic Acids Research, 1984, Vol. 12, No. 24 9567-9575
© 1984

MOLECULAR BIOLOGY

A method for measuring the non-random bias of a codon usage table

Andrew D. McLachlan, Rodger Staden and D.Ross Boswell

Medical Research Council Laboratoiy of Molecular Biology Hills Road, Cambridge CB2 2QH, UK

Received October 4, 1983. Revised November 13, 1984. Accepted November 13, 1984.

We describe a new statistical method for measuring bias in the codon usage table of a gene. The test is based on the multinomial and Poisson distributions. The method is used to scan DNA sequences and measure the strength of codon preference. For E. Coli we show that the strength of codon preference is related to levels of gene expression. The method can also be used to compare base triplet frequencies with those expected from the base composition. This second type of codon bias test is useful for distinguishing coding from non-coding regions.


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