DNApl is the language we use to define DNA libraries
Each DNApl file is comprised of three sections:
- Input section:
Defined between an "INPUT" tag and an "END" tag
All existing (and useful) fragments of DNA are written here. Please write any plasmid that you have, give it a name, and write down its full sequence (if available). Please only use sequenced plasmid.
- Definitions section:
This section is used the define sequences of DNA and give them a name. It is good practice to define each sequence beforehand and when sequences are used repeatedly throughout the library (for example Restriction Sites) it is also faster and prevents errors.
- Output section:
Defined between an "OUTPUT" tag and an "END" tag
The desired sequences are written here as a function of the inputs (and definitions). Some operations can be used including transformation viagra effects (mutations), concatenations (fusions) and expansion rules (multiple variants)
This is a very basic example showing only the three sections and the cutting operation.
T1_SsoPox := pte[1:808].loop1.pte[884:1023];
T2_AhlA := pte[1:808].loop2.pte[884:1023];
Graphic representation of DNApl
To get a better sense of how the DNApl is defined we represent is graphically like this:
You can see the output we defined. Each existing sequence is ovally shaped and each synthetic sequence is a square. Colors represent the different input fragments.
The operations that can be used
Extracts a part of a sequence
GENE1 := PLASMID[1000:2000];
- CONCATENATION (fusion)
Joins two sequences together
TARGET1 := EcoRI.GENE1.BamHI
- Amino Acid
Define a sequence by its aa sequence
GENE1 := a_a(VVPSTQPVTTPPATTPVTTPTIPPS);
See also example ebcell2 for how to define the codon table
Change a sequence in specific places
cer5_mut := cer5[90 =”A”, 354:356 = “ATG”];
Things to consider
- Have you specified all relevant inputs? It's better to give more input than give less.
- Restriction sites must be specified. Make sure they appear in the final graphics.
- Are there sequences that shouldn't appear at all? Restriction sites for example. This should be written in the DNApl