General explanation

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

Input

pte:=GAATTCATCACCAACAGCGGCGATCGGATCAATACCGTGCGCGGTCCTATCACAATCTCTGAAGCGGGTTTCACACTGACTCACGAGCACATCTGCGGCAGCTCGGCAGGATTCTTGCGTGCTTGGCCGGAGTTCTTCGGTAGCCGCAAAGCCCTAGCGGAAAAGGCTGTGAGAGGATTGCGCCGCGCCAGAGCGGCTGGCGTGCGAACGATTGTCGATGTGTCGACTTTCGATATCGGTCGCGATGTCAGTTTATTGGCCGAGGTTTCGCGGGCTGCCGACGTTCATATCGTGGCGGCGACCGGCTTGTGGTTCGACCCGCCACTTTCGATGCGATTGAGGAGTGTAGAGGAACTCACACAGTTCTTCCTGCGTGAGATTCAATATGGCATCGAAGACACCGGAATTAGGGCGGGCATTATCAAGGTCGCGACCACAGGCAAGGCGACCCCCTTTCAGGAGTTAGTGTTAAGGGCGGCCGCCCGGGCCAGCTTGGCCACCGGTGTTCCGGTAACCACTCACACGGCAGCAAGTCAGCGCGGTGGTGAGCAGCAGGCCGCCATTTTTGAGTCCGAAGGCTTGAGCCCCTCACGGGTTTGTATTGGTCACAGCGATGATACTGACGATTTGAGCTATCTCACCGCCCTCGCTGCGCGCGGATACCTCATCGGTCTAGACCACATCCCGCACAGTGCGATTGGTCTAGAAGATAATGCGAGTGCATCAGCCCTCCTGGGCATCCGTTCGTGGCAAACACGGGCTCTCTTGATCAAGGCGCTCATCGACCAAGGCTACATGAAACAAATCCTCGTTTCGAATGACTGGCTGTTCGGGTTTTCGAGCTATGTCACCAACATCATGGACGTGATGGATAGCGTGAACCCCGACGGGATGGCCTTCATTCCACTGAGAGTGATCCCATTCCTACGAGAGAAGGGCGTCCCACAGGAAACGCTGGCAGGCATCACTGTGACTAACCCGGCGCGGTTCTTGTCACCGACCTTGCGGGCGTCATGACTGCAG;

End

loop1 :=GATCTCTCACGATTATTGTTGCACAATCGACTGGGGAACTGCAAAACCAGAATATAAACCTAAGCTTGCTCCAAGATGGAGT;

loop2 :=GGCGCATGACGCGTCGTGTTTCATCGACTACTTCCCCAGCGCGGCAAGAGAAGTGGCACTTCCGAACTGGAAC;

Output

T1_SsoPox := pte[1:808].loop1.pte[884:1023];

T2_AhlA := pte[1:808].loop2.pte[884:1023];

End

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

• CUTTING
  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

• MUTATION
  Change a sequence in specific places
  cer5_mut := cer5[90 =”A”, 354:356 = “ATG”];

Things to consider

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