But any individual reverse translation may randomly be quite different. If you were to generate a new DNA over and over again, eventually this would create a collection of sequences where the average codon usage would exactly match the average for the. Each time you run the algorithm, a different, random set of codons will be selected. If you used this to optimize expression, the host would likely run out of that tRNA and you wouldn’t see optimal expression.įrequency Distribution – this selects a random codon for each amino acid, biased towards the most commonly used codon that encodes each amino acid. Perhaps this is only useful if you want to design a “best guess” primer and are willing to accept a certain failure rate. the most common Leu codon is CTC, all Leu codons will be CTC. Most Frequently Used Codon – this simply uses the most commonly occurring codon for each amino acid. There are four different algorithms that MacVector provides for optimizing codon usage. To use this function, you do need to supply a codon usage table – a number of common tables are shipped with MacVector: /Applications/MacVector/Codon Bias Tables/ However, MacVector also offers an optimization function if you are interested in designing a gene with codon usage optimized for expression in a particular organism. This is great if you want to identify less ambiguous sections to design probes or primers and in fact MacVector will even display a list of probes with the least ambiguities. The default option creates a DNA sequence with N’s and other ambiguities reflecting the degeneracy of the genetic code. The Analyze | Reverse Translation menu option lets you create a DNA sequence from a Protein sequence, reverse translated using a specific Genetic Code (by default, the Universal Genetic Code).
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