exCGen

exclusive Code Generator

(current)

Exclusive Code Generator (exCGen) is a tool for designing and screening DNA sequences. It identifies pairs of sequences with minimal binding free-energy from a pre-selected and screened set of sequences. The initial random sequence pool can be customized by inputting parameter and preset base information. For further information, please see: How it works

To effectively use DNA building materials, it is essential to carefully design their annealing order, which is determined by sequence. ExCGen is a tool that can aid in DNA design by generating mutually exclusive DNA blocks. For further information, please see: When to use it

✘
How it works

All strands were individually matched to calculate the free energy for specific and non-specific base pairing with each other. To determine the strongest pairing for all possible positions in structural variants*, the exCGen adopted an idea of the sliding algorithm (P.M. Vallone and J.M. Butler, (2004) Biotechniques, doi: 10.2144/04372ST03) and modified it to the matching process of bulged structures.

* For the structural variants, up to 3 bases in length for bulges and up to 7 bases in length for hairpins are tested in exCGen.

The level of base pairing was determined using the NN thermodynamics parameters (H.T. Allawi, J.Jr. SantaLucia (1997) biochemistry, DOI: 10.1021/bi962590c). If the non-specific binding free energy of a newly synthesized DNA strand is measured to be the lowest (stable) among all cases, but its value is less than the predetermined threshold (the ratio of non-specific ΔG (for self or cross) over specific ΔG (for duplex) in same length), the strand will be included in the list of completed sequences.

✘
When to use it

×
Completed sequences
No. Seq. Length GC(%) duplex_dG

Selected sequences
ID Seq. Length GC(%) duplex_dG
◈ Parameters
Length (mer)
min max
Pairs
min max
GC ratio (%)
0 100
◈ Thresholds
(?)
Remove sequence candidates that exceed the specified threshold [ΔG_nonspecific / ΔG_specific].
$\frac{ΔGhairpin}{ΔGpair}$ (%)
min max
$\frac{ΔGcross}{ΔGpair}$ (%)
min max
$\frac{ΔGselected}{ΔGpair}$ (%)
min max
◈ Preset bases
(?)
A : Adenine
C : Cytosine
G : Guanine
T : Thymine
R : G or A
Y : C or T
S : G or C
W : A or T
* : A or G
　　or C or T
(+) 5'-
-3'
◈ Exclusion bases
(?)
Bases that will not be included in the new sequence.
◈ Selected sequences
◈ Operation
◈ Dashboard

  • Start :
  • End :
    • -----------------------------------
  • Total
  • Pass (with Hairpin)
  • Pass (with Self-dimer)
  • Pass (with Completed)
  • Pass (with Selected)
  • Completion
  • Copy
    <=>
    ✔
    Completed sequences
    No. Seq. Length GC(%) duplex_dG

    Selected sequences
    ID Seq. Length GC(%) duplex_dG