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Code syntax for Free Design.

Type

Pattern

Description

End

::

End for circular DNA. When both ends are '::', the DNA will be recognized as circular.

End

:*B:

Blunt end with 5'-phophate.

End

:^B:

Blunt end without 5'-phophate.

End

:0B:

Hairpin end.

End

:^3TGA:

^ means no 5'-phosphate; ^3TGA means 3'TGA overhang.

End

:*5CCT:

* means 5'-phosphate; *3CCT means 3'CCT overhang.

Restriction Enzyme

[BamHI]

Example of a panlindromic restriction enzyme site.

Restriction Enzyme

[DraIII:CTG>

Example of a non-panlindromic restriction enzyme site. e.g. DraIII site is CACNNNGTG. The CTG in the pattern '[DraIII:CTG>' stands for the 'NNN'. The full sequence of this pattern '[DraIII:CTG>' is CACCTGGTG.

Restriction Enzyme

<DraIII:CTG]

Example of a non-panlindromic restriction enzyme site in reverse complementary form.
e.g. DraIII site is CACNNNGTG. The CTG in the pattern '[DraIII:CTG>' stands for the 'NNN'. The full sequence of this pattern '<DraIII:CTG]' is CACCAGGTG.

Feature

{Kan>

The kan feature.

Feature

<Kan}

The kan feature in its reversed complementary form.

Feature

{Kan:2-332>

The 2-332bp of the kan feature.

Feature

<Kan:2-332}

The 2-332bp of the kan feature in reversed complementary form.

Amino Acid

{KSTWN-

No '/'. '-' for stop codon.

The DNA sequence AAAAGCACCTGGAACTAA that corresponds the amino acid sequence KSTWN- due to optimized codon ratio.

Amino Acid

{KSTWN-/

With '/' at the end {????/. Forward form.

The DNA AAAAGCACCTGGAAC that corresponds to the amino acid sequence of KSTWN- due to optimized codon ratio.

Amino Acid

{/KSTWN-

With '/' at the end {/????. Reverse complementary form.

TTAGTTCCAGGTGCTTTT, the reverse complementary DNA sequence for the amino acid sequence of KSTWN- due to optimized codon ratio.

Comments

/* ..... */

Anything between /* and */ is the comment. It will not affect the resulting DNA.

Last edited Oct 5, 2015 at 5:25 PM by errisy, version 1