I. DNA Optimization
First, it performs DNA codon optimization based on the target organism by removing rare codons and replacing them with more prevalent codons.
(We noticed that many teams decided to utilize sequences from a variety of organisms such as firefly luciferase to ultimately be transformed into an experimentally “stable” organism.)
Secondly, the program checks the coding sequence for any restriction sites that are not allowed by the format specified by the user. After checking the sequence, MYS!S removes the restriction sites while ensuring that the modified sequence is still codon optimized.
In addition, it was pointed out that frequently a synthetic biologist would like to change specific amino acids in the DNA coding sequence. MYS!S decides what difference in nucleotide sequence are required to best make the amino acid change.
III. Restriction site analysis
Alternatively, an iGEMer might also want to add restriction sites to a DNA sequence in order to remove a particularly useful sequence. The program can handle this by either allowing the user to specify where the restriction site should be or by choosing what restriction site is desired and how sites need to be added to the sequence.