Home > Features > 2.Gene design

Gene design

 

Visual Gene Developer optimizes a gene construct and generates a lot of candidate gene constructs. Therefore, the first step to optimize a gene is to define a gene construct. Usually, a gene construct consists of several different gene components. For example, a gene construct may have three components such as Start codon, Target gene, and Stop codon that are orderly connected like [Start codon]-[Target gene]-[Stop codon]. At the same, a gene construct can have only single gene component like [Target gene]. In this case, a target gene may include both start codon and stop codon. Therefore, a gene construct contains at least one gene component.

 

In order to design a gene construct, the software has the 'Gene Construct Designer' window.

1. Click on the 'Gene construct' in the 'Project Explorer' window.

 

2. Click on the 'Add' button to add a new gene component, 'Delete' button to delete a current gene component, 'Move up'  or 'Move down' button to change the order of gene components.

3. Since gene component names are frequently used in many other sections to represent target gene components, we recommend you using  short names (below 10 letters).

4. There are four gene component types that are predefined in the 'Essential Script.vgs' file. Most user will use mainly 'Common coding region' or 'Non-coding region'. Most implemented algorithms also make use of these two component types.

Gene component type Feature Data format

 Common coding region

 Includes amino acid sequences

 Original AA: original amino acid sequence

 Original DNA: original DNA sequence

 Modified DNA: modified/optimized DNA sequence

 Non-coding region

 Pure DNA sequence

 Original DNA: original DNA sequence

 Modified DNA: modified/optimized DNA sequence

 Restriction enzyme site

 Single restriction enzyme site

 Original Format: string expression of restriction enzyme

 Original DNA: original DNA sequence

 Modified Format: modified/optimized string expression of restriction enzyme

 Modified DNA: modified/optimized DNA sequence

 Multiple cloning site

 Collection of restriction enzyme sites

 Original Format: string expression of restriction enzymes

 Original DNA: original DNA sequence

 Modified Format: modified/optimized string expression of restriction enzymes

 Modified DNA: modified/optimized DNA sequence

 

As shown in the table, every gene component should have 'Modified DNA' as a data format parameter because Visual Gene Developer (specifically predefined algorithms) uses this parameter to optimize and analyze gene sequences. Optimization process will modify DNA sequence of the 'Modified DNA' parameter value.

A user can define new gene component types like predefined ones. Check 'Module development' section in the left menu.