Codon Optimization Calculator:

As everyone who has studied biology in the last 30 years must know, proteins are made from mRNA which is made from DNA, and this is performed by a simple coding mechanism; a three base segment of DNA, called a codon, is translated into particular amino acid. Since there are 4 bases there are 4 x 4 x 4 = 64 possible codons. 3 of these codons in humans code for "stop", the end of a polypeptide chain. The other 61 code for particular amino acids. Since there are only 20 genetically encoded amino acids, most amino acids are coded for by multiple codons. Bacteria and mammals prefer to use different codons, so that mammalian genes frequently use codons which are rarely employed in bacteria. When this happens the mammalian gene may be expressed very poorly in bacteria, a significant problem. A way to deal with this is to look at the mammalian sequence, figure out which codons are optimal for bacterial expression, and synthesize an appropropriate DNA sequence specifically to efficiently express the mammalian gene in bacteria. This is time consuming to do by hand. An alternative is to set up software on your computer to do this. Or you could just use our simple on-line program which will not clog up your hard disk.

The program will ignore numbers, spaces or characters like B or Z which do not correspond to one of the 5 DNA bases. This program can also deal with FASTA format sequences (see here for info on that); it ignores any line of text which is started by a ">" character. The program can also process multiple FASTA format entries, only counting the sequence data and ignoring the stuff following the ">".
Select species you want to express your protein in: Bacteria Yeast Insect Mammalian

Do you want to add a stop codon? No Yes

Please type or paste your protein sequence in box below, can be upper or lowercase, program will read either and both.

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