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Optimal & Random mRNA Sequence Calculator

What does it do?

Finds the optimal mRNA sequence and a Random mRNA sequence based on codon usage frequencies and returns an alignment of the two.

How does the Optimal and Random mRNA Sequence Calculator work?

  • The website user enters an amino acid sequence using the one letter abbreviations along with a codon usage table from The Codon Usage Database website.
  • The calculator then returns the Optimal mRNA sequence and a Randomly generated mRNA sequence determined by the frequencies in the inputted codon usage table. 

What are the Optimal mRNA sequence and Randomly mRNA sequence?

  • Optimal mRNA sequence: always chooses the codon with the maximum frequency in the codon usage table.
  • Random mRNA sequence: uses the frequencies from the codon usage table to represent the probability that a certain codon will be selected.

How do I get a Codon Usage Table from the Codon Usage Database?

To get the codon usage table go to Codon Usage Database:

  • Select the organism you want the codon usage table for.
  • Highlight and copy the usage table like is done in the image below.

  • Paste the table into the codon usage table form on the previous page. Like is done below.

    • Enter the amino acid sequence in the next box.
    • Then press submit.

    What does the error message mean?

    If you received an error message and were told to visit this page most likely one of two things is wrong with your inputs, either:

    • The Amino Acid Sequence you inputted contains illegal characters. Double check that all characters in the inputted amino acid sequence are actual one letter abbreviations.
    • You may have not copied the entire codon usage table from The Codon Usage Database. Read the  instructions above about how to properly get the codon usage table.   

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