Home > Visual Gene Developer > 2.Menu and user interface

Menu and user interface


1. Main window menu: it includes most functions

2. Tool strip menu

3. Project Explorer: click on any item to show windows

4. Layer view manager: it shows information of a current gene construct graphically

5. Project window

6. Toolbox: click on any item to run it

7. Workspace: it contains a target sequence for gene analysis

8. Tool strip menu: almost all windows contain a localized tool strip menu



o Main window menu

 Visual Gene Developer 1.3 (Build 689)



o Summary

 Main window menu Description
 File  Open and save data file
 File > New project  Start new project
 File > Open project  Open existing project
 File > Save project  Save project file (file extension: vgp)
 File > Save project as  Save project file as
 File > Import Gene List > FASTA format  Import sequences from FASTA file
 File > Import Gene List > Regular text file  Import sequences from regular text file
 File > Import Gene List > View sample FASTA format file  
 File > Import Gene List > View sample Regular text file  
 File > Import Gene Construct List > Comma delimited standard text file  
 File > Export gene construct as > Comma delimited standard text file  Export to standard text format file
 File > Export gene construct as > Tab delimited standard text file  Export to standard text format file
 File > Copy gene construct > Only gene sequence  Copy gene sequence to clipboard
 File > Copy gene construct > Including full analysis result  Copy gene sequence to clipboard with analysis result
 File > Preference  Configure environment
 File > Exit  Exit
 Edit > Copy  Copy text of workspace window
 Edit > Paste  Paste to workspace window
 Edit > Search  Approximate sequence search (find similar sequences)
 Edit > Delete all gene constructs except current one  Initialize construct list in the 'Gene optimization' window
 Function > Parse sequence > Remove non-alphabetic characters  Parse text
 Function > Parse sequence > To DNA sequence  Parse text
 Function > Parse sequence > To Amino acid sequence  Parse text
 Function > Formatting > Space delimited  triplet  
 Function > Formatting > Replace U with T  
 Function > Formatting > Replace T with U  
 Function > Formatting > Convert to upper case  
 Function > Formatting > Convert to lower case  
 Function > Complementary sequence  Make complimentary sequence
 Function > Reverse sequence  Reverse source sequence
 Function > Reverse complementary sequence  Make complimentary sequence
 Function > Translate from DNA to amino acid  Translation
 Function > Back translate from amino acid to DNA  Back translation
 Function > Translate restriction enzyme  Convert restriction enzyme name into DNA sequence

 Function > Silent removal of sequences

 Perform silent removal of multiple sequences

  * Silent removal means a removal of certain target DNA sequence from a source sequence by replacing certain codons with synonymous codons while maintaining the expression of the same amino acids

 Function > Codon optimization

 Perform Monte-Carlo Codon Optimization (probability based random mutation)

 Function > mRNA optimization

 Perform mRNA Optimization combined with Codon Optimization

 Function > Degenerate gene sequence


 Function > File processing > Remove non-alphabetic letters in a file


 Data > Access to Kazusa Codon Usage Database (WEB)  Access http://www.kazusa.or.jp/codon/ directly
 Data > Access to Genomic tRNA Database (WEB)  Access http://gtrnadb.ucsc.edu/ directly
 Data > Make new codon usage and w table  Create new w table file
 Data > Lcal Codon usage and w table Library  Show w table library
 Data > Restriction enzyme library  Show restriction library window
 Analysis > Codon Usage Table  Build codon usage table

 Analysis > CAI, GC content, Nc

 Calculate several indexes such as CAI, GC content, Nc

 * CAI: Codon Adaptation Inex

    Nc: Number of effective codons

 Analysis > tRNA adaptation index (tAI)

 Calculate tAI

 Analysis > Search sequence  Search multiple sequences
 Analysis > Sequence comparison  Compare two sequences
 Analysis > Repeated sequence  Search repeated sequence
 Analysis > mRNA secondary structure  Calculate mRNA secondary structure
 Analysis > Batch analysis mode  
 Analysis > Gene optimization mode  
 Tool > Develop new module  Create new module
 Tool > Module Library  Show module library
 Tool > PropertyBag Library  Show PropertyBag library
 Tool > Artificial neural network  Show artificial neural network window
 Tool > GenBank Extractor  Extract field information from GenBank text file
 Network computing  
 Network computing > Server window  Show server control window
 Network computing > Job list  Show current job status of network computing
 Network computing > Add client  Add new clients
 Network computing > Shutdown clients  Close all active clients
 Window > Workspace  Show Workspace window
 Window > Gene analysis  Show Gene analysis window
 Window > Project window  Show Project window
 Window > Gene construct designer  Show Gene construct designer window
 Window > Configure gene optimization  Show Configuration of gene optimization window
 Window > Gene optimization main window  Show Gene optimization window
 Help > About  Show About window
 Help > Online website  Direct link to our software website