A protein-coding gene could be excludable, for instance, if it uses a genetic code that is unique to a particular group of organisms.
An increase in out-of-frame stops is therefore not a consistent advantage of using a genetic code with multiple stop codons.
The substitution matrices, JTT, WAG, LG, and KHG were estimated from nuclear DNA, which use a different genetic code from vertebrate mtDNA.
Because mitochondria use an alternative genetic code, all mitochondrial protein-coding transcripts are flagged as translation exceptions (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi SG5 for nonstandard codon usage specific to invertebrate mitochondria).
For example, Spironucleus, Trepomonas and Hexamita, form a monophyletic clade to the exclusion of Giardia in phylogenetic trees [ 24], and use an alternative genetic code whereby TAA and TAG, rather than being stop codons, encode glutamine [ 25, 26].
Previous research indicated that the small genomes of Hodgkinia and Zinderia use an alternative genetic code that has reassigned the UGA stop codon to tryptophan (McCutcheon et al. 2009b; McCutcheon and Moran 2010).
To minimize the problem generated by substitution saturation, nucleotide sequences can be translated into amino acid sequences; then they can be translated back into a nucleotide sequence using a standard genetic code, essentially getting rid of any synonymous substitutions.
Our procedure is a form of evolutionary design of experiments (Evo-DoE), building on previous work based on genetic algorithms, where experiments in each generation were specified by a genetic code, using genetic operators (mutations and crossovers) to generate new experiments for each successive generation [1] [5].
It could be based on DNA that uses a different genetic code, with perhaps more or fewer than four letters; it could be based on some complex molecule other than DNA, or more than the 20 amino acids from which our own proteins are made, or even some kind of chemistry based on something other than carbon and the other elements that we take for granted, like phosphorous or iron.
This phage display library uses a reduced genetic code to introduce sequence and conformational diversity into the antigen recognition loops of an antibody-like (Fab) scaffold [13], [14].
