Example 2

Calculate Gibbs energy of mRNA secondary structure and then screen out a given gene construct if calculated Gibbs energy is lower than the threshold value. It is a predefined script named as 'Check stable mRNA structure'

The module retrieves sequence information ('Target Gene Component ID') using GeneConstruct class and then generates lots of sequence segments 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 Gibb's free energy for each segment. If Gibb's energy is lower than a specified value ('Threshold value'), it returns 'Not pass' which means the gene includes stable mRNA secondary structure. If all sequence segments of the target gene are more unstable than the expected value ('Threshold value'), the module returns 'Pass'.

Step 1. Develop a new PropertyBag. Check a predefined 'mRNA Gibbs Energy Check' as shown in the figure

Because a user can't edit the PropertyBag, we show detailed setting in the below

Function Main()

     '*** Read parameters from PropertyBag ***********
     TargetGeneID=PropBag_Param.Value("Target Gene Component ID")
     SourceSeq=Get_SourceSeq(TargetGeneID)

     If SourceSeq="" then
          Main="Pass"
          Exit Function
     End If
     SourceSeq_Length=Len(SourceSeq)
     Start_Position=PropBag_Param.Value("Start position")
     End_Position=PropBag_Param.Value("End position")
     Window_Size=PropBag_Param.Value("Window size")
     Step_Size=PropBag_Param.Value("Step size")
     Unit=PropBag_Param.Value("Unit")
     Threshold_Value=PropBag_Param.Value("Threshold value")

     '*** Check parameters ***********
     If Start_Position<=0 then Start_Position=1
     If End_Position >SourceSeq_Length then End_Position=SourceSeq_Length
     If Start_Position>End_Position then
          TempValue=Start_Position
          Start_Position=End_Position
          End_Position=TempValue
     End If

     If Window_Size>100 then
          Window_Size=100
          PropBag_Param.Value("Window size")="100"
     End If
     If Window_Size<10 then
          Window_Size=10
          PropBag_Param.Value("Window size")="10"
     End If

     If Step_Size>100 then
          Step_Size=100
          PropBag_Param.Value("Step size")="100"
     End If
     If Step_Size<5 then
          Step_Size=5
          PropBag_Param.Value("Step size")="5"
     End If

     '*** Check mRNA Gibbs free energy ************************************************
     For Current_Position=Start_Position to End_Position - Step_Size step Step_Size   '<----- Moving window

          AppService.InstantMsg "Analyzing mRNA structure at " + CStr(Current_Position)

          TestSeq=Mid(SourceSeq,Current_Position,Window_Size)      '<---- Generates fragment of target gene
          TestSeq_Length=Len(TestSeq)
          Call mRNApredict.Calculate(TestSeq,True)

          GibbsEnergy=mRNApredict.GibbsFreeEnergy ()

          If Unit="Total energy" then
               If -GibbsEnergy > -Threshold_Value then
                    Main= "Not pass"
                    Exit Function
               End If
          Else
               If (-GibbsEnergy/TestSeq_Length) > -Threshold_Value then
                    Main="Not pass"
                    Exit Function
               End If
          End If
     Next

     Main="Pass"
End Function

Function Get_SourceSeq(TargetGeneName)       '<---- Get target sequence. Use this module as a template for module development
     TargetGeneConstructIndex=GeneConstruct.CurrentConstructIndex
     TargetGeneIndex=GeneConstruct.ComponentIndex(TargetGeneConstructIndex,TargetGeneName)
     Get_SourceSeq=GeneConstruct.ParameterValue(TargetGeneConstructIndex,TargetGeneIndex,"Modified DNA")
End Function