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Table 4 Comparison of synonymous substitution numbers at paired and unpaired sites.

From: Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

  

ATOpt

ATNopt

AT

GCOpt

GCNopt

GC

All

(1)

MFE

0.511

NS

0.542

NS

0.600

NS

0.488

NS

0.296

NS

0.414

NS

0.481

NS

 

Mc

0.567

NS

0.528

NS

0.546

NS

0.544**

0.327*

0.458**

0.505

NS

(2)

MFE

0.255

NS

0.201

NS

0.232

NS

0.140

NS

0.257

NS

0.213

NS

0.225

NS

 

Mc

0.255

NS

0.230

NS

0.238

NS

0.264

NS

0.167

NS

0.222

NS

0.232

NS

  1. Looking at S. cerevisiae and S. paravensis , I compare numbers of each codon in S. cerevisiae being either synonymous non-conserved or conserved at paired or unpaired sites. Structure prediction is based on RNAfold upon the S. cerevisiae sequence using MFE and McCaskill's (Mc) algorithm. Mantel Haenzsel estimators and significances are presented. WMH<1 = lower numbers of synonymous substitutions at paired sites. (1) All genes, (2) Genes that are shorter than 800 bp.
  2. * < 0.05, ** < 0.01, *** < 0.005, NS = not significant