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Select Optimization Criteria For Current Job:
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Codon Auto-Correlation
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The codon autocorrelation option accounts for the correlation between consecutive synonymous codons that may be separated by any number of codons encoding other amino acids. It is recommended that this option is used together with ICU. A target value of 1 maximizes the appearance of the same synonymous codons consecutively.
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Optimize by Codon Auto-Correlation with target value of:
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5' RNA Folding Instability
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CoDOn can optimize by RNA folding instability. If you maximize instability, the RNA is less likely to fold on itself, allowing the ribosome easier access for initiation. Because calculating folding energy for the whole RNA strand is time-consuming, we limit calculations to the first 10 to 50 bases on the 5' end, where translation initiation occurs.
Warning: Enabling this option will greatly increase the computation time required.
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Limit RNA folding energy calculations to a window of the first
bases
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GC Content (Total and GC3)
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Total GC content refers to the GC content of the entire sequence. GC3 content refers to the GC content of only the 3rd base of all codons in the sequence. The 1st and 2nd bases are completely ignored. (E.g. the sequence ATGTGGTAA will have a GC3 content of 2/3 = 66.67%.)
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Optimize Total GC content with target percentage:
%
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Optimize GC3 content with target percentage:
%
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Choose Either To:
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Use Inbuilt Expression Host
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Selecting an inbuilt expression host will also automatically use the corresponding Translation Rules for that host. You may use all or only a subset of the genes, from your desired target expression host. Selection of which genes you want to use can be done on the next page.
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Target Expression Host:
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Or:
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Input Custom Codon Usage Pattern Values
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Optional: Codon Context Usage Pattern (Sample Format)
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