About Codon Optimization
Important: As of 22 Mar 2016, COOL has changed URL. Please update your bookmarks.

Codon Optimization On-Line (COOL) can be used to design a nucleotide sequence for improved expression of the desired protein within the target host organism. This method is useful for life science research, especially in the area of synthetic biology, where there is a need to achieve high expression of a foreign or artificial gene within a non-native host.

There are several methods of calculating the optimal output sequence. This web tool is an online implementation of the algorithm described in our previous publication (Chung BKS and Lee DY. Computational codon optimization of synthetic gene for protein expression. BMC Systems Biology 6:134). It has been further augmented to include additional optimization criteria, and multiple output sequences within pareto space. You may view an example of this pareto spatial distribution of results, by generating a new sample output dataset. Details on how this example was generated can be found in our guide.

Please Cite: Chin JX, Chung BKS and Lee DY (2014). Codon Optimization On-Line (COOL): a web-based multi-objective optimization platform for synthetic gene design. Bioinformatics, 30 (15): 2210-2212, doi: 10.1093/bioinformatics/btu192 (link)

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22 Nov 2016: We have updated the list of sample genes for Escherichia coli, Pichia pastoris and Saccharomyces cerevisiae.

8 Nov 2016: There has been a significant code overhaul in preparation for the new workflow. Let us know if you spot any errors.

28 Oct 2016: We have added CpG and GC3 optimization to COOL.

23 Aug 2016: We have added optimization by Codon Auto-Correlation to COOL.

7 Jul 2016: COOL has been upgraded to allow optimization by 5' RNA folding instability.

13 Jun 2016: Shine-Dalgarno mRNA and Kozak sequence added as options to the Exclusion Sequence dropdown menu.

30 May 2016: In addition to repeats that occur consecutively, COOL can now screen for motifs of a specified length, which occur repeatedly, regardless of location.

24 May 2016: COOL now accepts sequences which do not end with stop codons. However, if you exclude the stop codon, it will likewise be absent in the optimized results, which may cause translation runoff.

23 May 2016: Exclusion Sequences (under section 4: Motif Settings) can now include any ambiguous nucelotide base.

22 Mar 2016: The URL for COOL has changed. Please update your bookmarks.

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