Drummond:Akashi's Test

Akashi's Test for Translational Accuracy

Akashi's test is very simple. Suppose you have two aligned codon sequences (a target sequence and an orthologous sequence) and a list of optimal codons. The question is, is there an association between optimal codons and conserved amino acids, controlling for expression level, amino acid usage, etc.?

From the aligned codon sequences, build a 2x2 table with entries a, b, c, and d like this:

AA=Ser	Conserved	Variable
Preferred	a	b
Unpreferred	c	d

for each amino acid. You'll usually have 18 tables; W and M have no synonymous codon alternatives and therefore don't contribute to Akashi's test.

• a = the number of codons in your target sequence that encode amino acid AA, are OPTIMAL, and encode an AA which is unchanged (CONSERVED) in the orthologous sequence
• b = the number of codons in your target sequence that encode amino acid AA, are OPTIMAL and encode an AAwhich is different (VARIABLE) in the orthologous sequence
• c = the number of codons in your target sequence that encode amino acid AA, are NON-OPTIMAL and encode an AA which is unchanged (CONSERVED) in the orthologous sequence
• d = the number of codons in your target sequence that encode amino acid AA, are NON-OPTIMAL and encode an AA which is different (VARIABLE) in the orthologous sequence

References

1. Akashi H. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics. 1994 Mar;136(3):927-35. DOI:10.1093/genetics/136.3.927 |