Table 4

Comparison of synonymous substitution numbers at paired and unpaired sites.


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

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.

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

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