Home > Features > 4.Gene optimization

Gene optimization

 

Visual Gene Developer provides several algorithms to optimize gene constructs and find the best candidates.

Here is a summary of implemented algorithms.

 Module name

 Module category

 Description

 Monte-Carlo Codon Optimization

 Sequence optimization

 Predefined probability (defined in w-table file) based random mutation (=Monte-Carlo simulation). Target codons will be replaced by new codons that have different probability.

 It checks following functions to screen out candidate gene constructs

(Check CAI, Check restriction enzyme site, Check repeated sequence,  Check excluded sequence)

 Local mRNA Optimization mRNA structure optimization  Adjust mRNA Gibbs energy to be in the specified range given by lowest Gibbs Energy (AvgBaseGibbs_Low) and highest Gibbs Energy (AvgBaseGibbs_High). It modified sequence performing Codon optimization or synonymous substitution.A user can set the target range given by Start and End locations in a sequence.
 mRNA Profile Optimization mRNA structure optimization

 Improved from Do_mRNAOpt_ProbabilityRandom. It optimizes a mRNA Gibbs energy profile along a long sequence. A moving window method was adopted.

 Local mRNA Profile Optimization mRNA structure optimization  Modification of Do_mRNAProfileOpt. A user can set the target range given by Start and End locations in a sequence.
 Silent removal v1

Gene manipulation

 Remove undesired sequences. Can specify up to 10 sequences.
 Silent removal v2

Gene manipulation

 Remove undesired sequences. Can process multiple query sequences.
 Silent removal of potential polyadenylation sites

Gene manipulation

 Remove predefined sequences of potential polyadenylation signal sequences

 Silent removal of potential intron cryptic splice sites

Gene manipulation

 Remove predefined sequences of potential intron cryptic donor and receptor signal sequences

 Check CAI

 Constraint

 Return 'Not pass' if CAI value is lower than set point

 Check restriction enzyme site

 Constraint

 Return 'Not pass' if sequence contains certain restriction enzyme sequence

 Check repeated sequence

 Constraint

 Return 'Not pass' if sequence contains certain number of repeated sequence

 Check excluded sequence

 Constraint

 Return 'Not pass' if sequence contains certain excluded sequence

 Check stable mRNA structure

Constraint

 Return 'Not pass' if sequence contains stable mRNA secondary structures

 

 The module retrieves sequence information and then generates lots of sequence segment specified by 'Window size'. The moving window scans along the sequence with a given 'Step size'. The Visual Gene Developer predicts mRNA secondary structure and calculates Gibbs free energy for each segment. If Gibbs energy is lower than a specified value ('Threshold value'), it returns 'Not pass' that means the gene includes stable mRNA secondary structure. If all sequence segments of target gene are more unstable than the expected value ('Threshold value'), the module returns 'Pass'.

For more details about 'Module category', check 'Module development' section in the left menu. At the same time, all predefined modules were summarized in 'Class & module' section in the left menu.

 

Important!  

Method 1 (Working on 'Workspace'): Paste sequence to 'Workspace' window and then click on 'Function > Codon optimization'. You will see 'Codon optimization' window. Adjust parameters and then click on 'Perform' button. For mRNA structure optimization, click on 'Function > mRNA optimization'. You will see 'mRNA optimization' window. Adjust parameters and then click on 'Analyze' button and then 'Optimize' button

Method 2 (Working on Gene construct): Firstly, configure optimization condition in the 'Configuration of gene optimization' window and then do optimize a gene construct in the 'Gene optimization' window.

 


o Method 1

o Simply way to optimize codon on 'Codon optimization' window

1. Paste any sequence to the 'Workspace' window

2. Click on the menu item (Menu: Function > Codon optimization)

3. A window titled 'Codon optimization' will be shown.

4. Click on the 'Perform' button

5. Click on the 'Apply and Close' button

 

 

o Simply way to optimize codon on 'mRNA optimization' window

1. Paste any sequence to the 'Workspace' window

2. Click on the menu item (Menu: Function > mRNA optimization)

3. A window titled 'mRNA optimization' will be shown.

4. Click on the 'Perform' button

5. Click on the 'Optimize' button

6. Check results and click on 'Apply' button.

7. You can check mRNA profile clicking on the 'Draw' button

 

 


o Method 2

o How to configure optimization condition

1. Click on the 'Configuration' item in the 'Project Explorer' window.

2. A window titled 'Configuration of gene optimization' will be shown.

3. Click on one of items.

4. Choose one of algorithms.

 

 

5. In addition, you may click on the 'Constraint'

6. Choose one of algorithms

7. Adjust parameters. For example, when you click on the 'On' checkbox, it will deactivate a selected module and an optimization algorithm will neglect inactivated items.

 

o More details about gene optimization procedure

There are 4 different categories of optimization condition such as 'Sequence optimization', 'mRNA structure', 'Manipulation', and 'Constraint'.

It's up to you to classify the module to one of them. However, internal algorithms orderly proceed from 'Sequence optimization' to 'Constraint'. Therefore, 'Sequence optimization' has the highest priority than other conditions and 'Constraint' is the lowest priority. For more details, check 'Module development' section in the left menu.

 

 

o How to optimize gene construct

 

1. Click on the 'Configuration' item in the 'Project Explorer' window.

2. A window titled 'Configuration of gene optimization' will be shown. Choose algorithm and click on the 'Run' button. If you want to stop optimization, click on the 'Stop' button.

 

As shown in the figure, 'Automated conditional search' algorithm produces a lot of candidates that fit for the condition defined in 'Constraint' in the 'Gene optimization condition' window.

3. Because optimization algorithm initially starts from a selected gene construct (=there are a parent gene construct and lots of child gene constructs), simply choose a gene construct clicking in the table and then start a new optimization cycle.

4. If you want to re-define table, click on the 'Viewer setting' button in the 'Gene optimization' window.

5. Add/Delete functions in 'Viewer setting' window.

 

 


o How to develop custom gene optimization module?

 

The software supports developing user-defined new algorithms for gene optimization. Module development section in the left menu will be much helpful. Basically, users can access the gene construct memory array using a class (class name: GeneConstruct) to modify sequence.

Check the following example.

 

1. Click on the 'Module Library' in the 'Tool' menu

2. Choose 'GeneConstruct.ParameterValue' in the 'Module Library' window

3. Click on the 'Edit Module' button

4. You can see the 'Module Editor' window. Click on the 'Test run' button

5. Check the result and source code.

 

 

Source code

VBScript

Function Main()
   GeneComponentName=GeneConstruct.ComponentName(1,3)     '<---  Get 3rd gene component name of the first gene construct

   GeneSequence=GeneConstruct.ParameterValue(1,3,"Modified DNA")     '<---  Get parameter value of modified DNA

   Msgbox GeneComponentName + " = " + GeneSequence    '<---  Show result consisting component name and its sequence

End Function