All genes of living organisms are translated into proteins according to a single genetic code. Eighteen out of the twenty amino acids are encoded by multiple codons, called synonymous codons. If the ultimate goal of protein translation is to produce the encoded amino acid, each synonymous codon should be used equally. Interestingly however, biased usage among synonymous codons occurs in organisms like Escherichia coli and yeast. Codon usage bias refers to the fact that some synonymous codons are used more frequently than others when encoding the same amino acid. Very little is understood about codon usage bias in vertebrates. It is known that natural selection preserves amino acids in proteins that have vital biological functions, but whether or not natural selection acts directly on synonymous codons is unclear.
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We developed a program to collect genomic data from the public database, NCBI. The program compares codon usage bias between conserved and non-conserved amino acids and between specific species of vertebrates. The codon usage from each homologous group of proteins were aligned using MUSCLE which allowed for the conserved and non-conserved amino acids to be identified. Codon usage bias was then assessed using relative synonymous codon usage (RSCU), which is the number of times a codon appears in a gene divided by the expected occurrences under equal codon
We developed a program to collect genomic data from the public database, NCBI. The program compares codon usage bias between conserved and non-conserved amino acids and between specific species of vertebrates. The codon usage from each homologous group of proteins were aligned using MUSCLE which allowed for the conserved and non-conserved amino acids to be identified. Codon usage bias was then assessed using relative synonymous codon usage (RSCU), which is the number of times a codon appears in a gene divided by the expected occurrences under equal codon