For each resampled genome, each open reading frame is resampled independently, thereby all synonymous codons inside one open reading frame are reshuffled randomly.
We then used ANNOVAR software (Wang et al., 2010) to functionally annotate the variants and thereby identify non-synonymous substitutions, splicing mutations or mutations in 3′UTR or 5′UTR.
Importantly, any mutation operator targeting gene-coding sequences can be further constrained to only generate synonymous mutations, thereby preserving the encoded protein sequence while modifying the underlying DNA properties.
These results support our previous findings (e.g. [ 21]) that filtering synonymous substitutions (and thereby compositional heterogeneity) can result in more robust phylogenetic inference at deep levels.
The variable granularity of ICD-9 coding may also explain the generation of synonymous health problems, thereby inflating for some patients, the number of health problems automated by the system and the number of those that were rejected.
More recently, Isaacs et al. [85] reported the replacement of all 314 TAG stop codons present in the genome of E. coli with synonymous TAA codons, thereby demonstrating that massive substitutions can be combined into higher-order strains without lethal effects.
Alternatively, a special chromatin structure of imprinted genes might reduce overall mutation rates in the germ lines, thereby leading to the observed lower synonymous substitution rates.
Nucleotide substitutions can either be nonsynonymous (i.e. protein changing, thereby potentially impacting the fitness) or synonymous (i.e. not protein changing, thereby theoretically without consequences for the fitness).
Investigating a potential functional role of the variants included in this study, revealed that rs2286936 of ACADL is a non-synonymous coding variant and thereby could impact on the measured phenotypes.
Amplification is achieved by pairing non-degenerate codon positions of two or more overlapping sequences, thereby maximizing the probability of non-synonymous substitutions.
The advantage of these methods is that they use amino acid sequences, and thereby is not sensitive to saturation of synonymous sites.
