14TSB_SynBio: BaseHunter: a software tool for synthetic biology procurement

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Proteins are encoded into DNA using four chemical bases (A, T, C and G). A string of three bases is called a codon. SinceDNA has four bases, a maximum of 64 (4x4x4) unique codons can be formed. Of the 64 possible codons, 61 are used toencode amino acids. There only 20 different amino acids used to construct proteins. Rather than having unused codons,life uses a system in which an average of three different codons encode the same amino acid. Consequently, the sameprotein sequence can be encoded with many different DNA sequences. Each DNA sequence will vary with respect toparameters such as translational efficiency, transcriptional efficiency, protein folding and ease of synthesis. Codonoptimisation is an algorithmic process that seeks to pick the best possible variant for a given purpose. The research part ofthis project seeks to develop a way of measuring how well different codon optimisation algorithms perform. This will bedone by obtaining different codon optimised genes and measuring how they behave in living systems.