General explanation


DNApl is the language we use to define DNA libraries


Each DNApl file is comprised of three sections:

  1. 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.
  2. 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.
  3. 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)



An Example

This is a very basic example showing only the three sections and the cutting operation.

More examples can be seen here










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
    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


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