Settings File

The settings.json file controls basic properties of sequences generated, and looks like this:

{
        "alphabet DNA"                          : "ACGT",
        "alphabet RNA"                          : "ACGU",

        "PCR-screen DNA sequences"      : "No"
}

• "alphabet DNA" specifies the DNA alphabet to use. The default is the four bases ACGT. However, restricted alphabets can be used, like ACT.

Note

This setting only applies to generating DeBruijn sequences and random sequences.

• "alphabet RNA" specifies the RNA alphabet to use, similar to above.

Note

This setting only applies to generating DeBruijn sequences and random sequences.

• "PCR-screen DNA sequences" is a "Yes"/"No" option. When "Yes", DNA sequences have to pass a PCR primer check before being added to a generated sequence pool. See the PCR Primer Check documentation page.

Note

• Setting this option to "Yes" slows down DNA sequence generation, as more sequences have to be generated (some are rejected) and all sequences require additional checking.

• RNA sequences are not directly amplified by PCR and thus do not undergo a PCR check.