Genetic Constructor

The Genetic Constructor Support Hub

Welcome to the Genetic Constructor developer hub. You'll find comprehensive guides and documentation to help you start using and extending the Genetic Constructor as quickly as possible, as well as support if you get stuck. Let's jump right in!

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GSL Levels and Operators

Using the GSL Operators in the Genetic Constructor

In the Genetic Constructor you have 3 ways to use the operators:

  • You can type them from memory
  • You can drag&drop them from the GSL symbol library
  • You can make use of the snippets within the editor of the GSL extension

The symbol library is to be found in the left vertical bar - you may have to unfold it. First begin typing your favorite gene (MFG) into the editor and then drag, for example, the promoter symbol on top. It will create pMFG. If you add the inversion symbol you should now get pMFG! and so on.

Level 0

Is the literal DNA sequence including IUPAC nucleotides.

Level 1

Assuming the following conventions and an annotated reference genome level 1 syntax can be translated into level 0 unambiguously.

Gene parts

g

prefix

gene locus

p

prefix

promoter part

t

prefix

terminator part

u

prefix

upstream part

d

prefix

downstream part

o

prefix

open reading frame

f

prefix

fusible ORF, no stop codon

m

prefix

mRNA

[]

postfix

slice of a gene locus

S or E

postfix

slice coordinate relative to the Start of the End of an open reading frame

!

prefix

invert sequence orientation

Other

Symbol
Position
Description

###

inline

marker sequence

~

prefix

approximate coordinate

~

inline

heterology block

/.../

inline

insert custom bases

/$.../

inline

insert custom peptides

@

prefix

reference external part

&

prefix

reference a defined variable

Level 2

Specifies concrete components, but leaving considerable freedom in the concrete construction placement up to the compiler.

Symbol
Position
Description

$

postfix

amino acid mutation

*

postfix

nucleotide mutation

^

postfix

gene knockout

>

infix

promoter replacement or over-expression

.

infix

namespace qualifier

Level 3

The most abstract level that allows the compiler to not only determine the exact positions, but also chose parts. For example gNeutral selects a gene locus with a gene that is not essential to the organisms. pStrong would have the compiler select a strong promoter. So gNeutral^ ; pStrong>gMFG would replace a neutral gene with "my favorite gene" under the control of a strong promoter.

GSL Levels and Operators