Table 2

Comparison of conserved optimal codon numbers at paired and unpaired sites.

RNAfold (S. cerevisiae)
 ALIfold


MFE
 Mc
 MFE
 Mc
Amino acids with GC-ending optimal codons
LeuTTG
 1.380 ***
 1.273 ***
 1.811 ***
 1.456 ***
LysAAG
 1.772 ***
 1.654 ***
 2.019 ***
 1.654 ***
PheTTC
 1.075 ***
 1.120 ***
 0.786 NS
 0.864 **
TyrTAC
 0.809 NS
 0.720 NS
 0.741 NS
 0.631 NS
HisCAC
 0.707 NS
 0.600 NS
 0.568 NS
 0.657 *
AspGAC
 0.813 NS
 0.838 NS
 0.656 ***
 0.746 **
AsnAAC
 0.891 *
 0.831 NS
 0.725 **
 0.637 NS
Amino acids with one GC- and one AT-ending optimal codon
IleATC
 1.318 ***
 1.254 ***
 1.555 ***
 1.049 ***
IleATT
 1.272 ***
 0.978 ***
 1.561 ***
 1.009 ***
ValGTC
 0.585 NS
 0.852 ***
 0.734 ***
 0.560 ***
ValGTT
 0.705 *
 0.794 NS
 0.806 *
 0.686 NS
ThrACC
 0.838 **
 0.921 ***
 0.811 ***
 0.750 ***
ThrACT
 0.940 ***
 0.876 ***
 0.932 ***
 0.655 ***
SerTCC
 0.614 NS
 0.668 NS
 0.583 NS
 0.591 NS
SerTCT
 0.794 NS
 0.816 NS
 0.816 ***
 0.985 ***
Amino acids with AT-ending optimal codons
AlaGCT
 0.968 **
 0.904 ***
 1.073 ***
 0.883 ***
ArgAGA,CGT
 0.588 ***
 0.545 ***
 0.518 ***
 0.460 ***
GlyGGT
 0.894 NS
 0.779 NS
 0.901 ***
 0.752 NS
GlnCAA
 0.442 ***
 0.353 ***
 0.293 ***
 0.278 ***
GluGAA
 0.946 ***
 0.350 ***
 0.386 ***
 0.315 ***
ProCCA
 0.851 NS
 0.734 NS
 0.729 **
 0.689 *
CysTGT
 0.500 NS
 0.382 NS
 0.755 ***
 0.403 NS

Separately for each amino acid, I combine contingency tables of the different genes. Mantel Haenzsel estimators and significances are presented, with WMH <1 = lower optimal codon use at paired than at unpaired sites. Structure prediction is based on ALIfold and RNAfold using MFE and McCaskill's (Mc) algorithm.

* < 0.05, ** < 0.01, *** < 0.005, NS = not significant

Stoletzki BMC Evolutionary Biology 2008 8:224   doi:10.1186/1471-2148-8-224