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However, the most used codons did not always have a corresponding tRNA in the mt genome even when the wobbling rule was taken into account (Crick 1966), (http://www.ncbi.nlm.nih.gov/books/NBK21424/).nih.gov/books/NBK21424/
For example, the most representative motifs GCA/TGC, AAG/CTT and AGC/GCT are also found among the most used codons GCA, AAG and AGC (20.7%, 33.6% and 15%, respectively).
Indeed the steady state concentrations within the cell of the major tRNAs (reading most used codons) must be higher than those of minor tRNAs (reading rare codons).
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Most used codon is UUA (Leu), while less used codon is CGC (Arg).
Various terms have been used to describe the most used codon for amino acids.
The A-T content of ORF117 is 59.83% and the most used codon is UUU (Phe), with 7 hits.
Conversely, ORF195 is not found by Glimmer and has a higher A-T content than ORF117 (73.33%); consistently, the most used codon is AAA (Lys).
The maximum value of 1 is only achieved if, for each synonymous codons set, all amino acids in the considered gene are encoded by the most used codon in the reference set.
Moreover, notwithstanding the low (for S. velum) A-T content, the most used codon is UUU (Phe), which is also among the most used ones in all PCGs of this mtDNA, and therefore its codon composition is similar to that of other PCGs.
ORF195 was not confirmed by Glimmer, but SignalP could retrieve a weak similarity with a signal peptide in the first 29 amminoacids of the putative translated protein; the A-T content of ORF195 is 73.33% and the most used codon is AAA (Lys), with 12 hits.
In this study, we calculated total codon usages and identified the most frequent and most seldom used codons.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com