• Back to Genome Compiler
  • Genome Compiler Manual
  • Cover
  • 1. Using Genome Compiler
    • 1.1. Getting Started
      • 1.1.1. Creating an Account
      • 1.1.2. Logging in
    • 1.2. Genome Compiler User Interface
      • 1.2.1. Overview of Genome Compiler User Interface
      • 1.2.2. Understanding Genome Compiler's Terminology
      • 1.2.3. Customizing the Workspace Layout
      • 1.2.4. Project Views
      • 1.2.5. Tooltips
      • 1.2.6. Numbering of Base Pairs and Amino Acids
      • 1.2.7. Annotation Layers Menu
      • 1.2.8. Viewing "More Properties"
      • 1.2.9. Help and Preferences
      • 1.2.10. Take a Snap Shot
    • 1.3. Integrated Sequence Libraries
      • 1.3.1. Genome Compiler Library
      • 1.3.2. Genome Compiler's Auto Annotations Library
      • 1.3.3. Sample Projects
    • 1.4. Importing and Exporting
      • 1.4.1. Importing DNA and Protein Sequences
      • 1.4.2. Importing Parts
      • 1.4.3. Exporting Files
      • 1.4.4. Importing Alignments
      • 1.4.5. Importing Primers
      • 1.4.6. Exporting Primers
      • 1.4.7. Troubleshooting
    • 1.5. Basic Sequence Editing
      • 1.5.1. Basic Copy/Cut/Paste/Delete/Undo/Redo
      • 1.5.2. Drag and Drop Functionality
      • 1.5.3. Adding New Parts
      • 1.5.4. Adding Amino Acids
      • 1.5.5. Mutating Amino Acids
      • 1.5.6. Reverse Complement
      • 1.5.7. Merging and Splitting Parts
      • 1.5.8. Selecting Strand
      • 1.5.9. Basic Local Alignment Search Tool (BLAST)
      • 1.5.10. Single Parts in the Materials Box
      • 1.5.11. Linearize and Circularize
    • 1.6. "Go to" a region in the sequence
      • 1.6.1. Opening the "Go to" Dialog
      • 1.6.2. "Go to" Dialog
    • 1.7. Search in the Materials box
      • 1.7.1. Searching in the Materials box
      • 1.7.2. Example
    • 1.8. Search in Projects
      • 1.8.1. Searching in Projects
      • 1.8.2. Advanced Search
    • 1.9. NCBI Search
      • 1.9.1. Searching in the NCBI Database
      • 1.9.2. Importing NCBI files
    • 1.10. Sharing and Collaboration
      • 1.10.1. Cloud Folders
      • 1.10.2. Creating New Folders
      • 1.10.3. Creating Subfolders
      • 1.10.4. Sharing Folders
    • 1.11. User Comments
      • 1.11.1. User Comments Indicator and Tooltip
      • 1.11.2. Displaying and Navigating to User Comments
      • 1.11.3. Adding Comments
      • 1.11.4. Multiple Users making Comments in a Single Project
      • 1.11.5. User Comments Summary Table
    • 1.12. Track Changes
      • 1.12.1. Track Changes Indicator and Tooltip
      • 1.12.2. Displaying and Navigating to Tracked Changes
      • 1.12.3. Multiple Users making Changes in a Single Project
      • 1.12.4. Track Changes Summary Table
    • 1.13. Ordering and Pricing
      • 1.13.1. Pricing for Projects
      • 1.13.2. Pricing for Primers
    • 1.14. Compilation
      • 1.14.1. Selecting Rules for Activation
      • 1.14.2. Compiling Projects
      • 1.14.3. Error and Warning Indicators
      • 1.14.4. Compilation Summary Table
      • 1.14.5. Navigating to Errors and Warnings
    • 1.15. Back Translation
      • 1.15.1. Changing the Project Host Organism
      • 1.15.2. How to Back Translate a Part
      • 1.15.3. Back Translation Settings
    • 1.16. Combinatorial Design
      • 1.16.1. Circuit Part Combinatorial
      • 1.16.2. Protein Engineering Combinatorial
    • 1.17. Managing Restriction Sites
      • 1.17.1. Opening the Restriction Sites Settings Dialog
      • 1.17.2. ”Restriction Site” Settings Dialog
    • 1.18. Virtual Digest
      • 1.18.1. Opening the Virtual Digest Dialog
      • 1.18.2. "Run Digest" Dialog
      • 1.18.3. "Digest" Results
      • 1.18.4. Gel simulation
    • 1.19. Primer Design
      • 1.19.1. Viewing Primers in Genome Compiler
      • 1.19.2. Opening the Primer Design Dialogs
      • 1.19.3. Manual Primer Design Dialog
      • 1.19.4. Editing and Deleting Primers in Projects
      • 1.19.5. Primer Pairs
      • 1.19.6. Auto Design Primers Dialog
      • 1.19.7. Primer Summary Table
    • 1.20. Primer Libraries
      • 1.20.1. Creating and Opening Your Primer Libraries
      • 1.20.2. Importing and Adding Primers to Primer Libraries
      • 1.20.3. Attaching Primers to a Project
      • 1.20.4. Editing and Deleting Primers in Primer Libraries
    • 1.21. Cloning Wizard: Restriction Ligation
      • 1.21.1. Opening the Cloning Wizard for Restriction Ligation
      • 1.21.2. Select Cloning Procedure
    • 1.22. Cloning Wizard: Gibson Assembly
      • 1.22.1. Opening the Cloning Wizard for Gibson Assembly
      • 1.22.2. Select Cloning Procedure
      • 1.22.3. In-house Gibson Assembly: Select Backbone
      • 1.22.4. In-house Gibson Assembly: Select Backbone: Linearise by Digest
      • 1.22.5. In-house Gibson Assembly: Select Backbone: Linearise by PCR
      • 1.22.6. In-house Gibson Assembly: Select Backbone: Linearise by Sequence Position
      • 1.22.7. In-house Gibson Assembly: Select Fragments and spacers
      • 1.22.8. In-house Gibson Assembly: Generate Fragments by "PCR"
      • 1.22.9. In-house Gibson Assembly: Generate Fragments by "Synthesis"
      • 1.22.10. In-house Gibson Assembly: Finalize
    • 1.23. ORF Detection
      • 1.23.1. Opening the ORF Settings Dialog
      • 1.23.2. ORF Settings Dialog
      • 1.23.3. Activating the ORF finder
      • 1.23.4. Viewing ORFs
    • 1.24. Sequence Alignment
      • 1.24.1. Opening the Alignment Settings Dialog
      • 1.24.2. Using the Alignment Settings Dialog
      • 1.24.3. Alignments Summary Table
      • 1.24.4. Viewing Alignment Sequences
      • 1.24.5. Editing Alignment Sequences
    • 1.25. Auto annotation
      • 1.25.1. Auto Annotation libraries
      • 1.25.2. How to add/import annotations to custom Auto Annotation libraries
      • 1.25.3. How to Auto Annotate Sequences
      • 1.25.4. Auto Annotation Settings Dialog
      • 1.25.5. Viewing and Editing Annotations
    • 1.26. Project Annotations
    • 1.27. Melting Temperature (Tm)
    • 1.28. RBS Calculator
      • 1.28.1. Opening the RBS Calculator
      • 1.28.2. Choosing the Desired RBS Mode
      • 1.28.3. Reverse Engineer mRNA Sequence
      • 1.28.4. Analyze a RBS
      • 1.28.5. Design a Synthetic RBS
      • 1.28.6. Design Synthetic RBS with Constraints
      • 1.28.7. View RBS Results
    • 1.29. Genome Compiler Support
  • 2. Step by Step Workflows
    • 2.1. Auto annotating Sequences
    • 2.2. Gene Amplification
    • 2.3. Cloning
    • 2.4. Manual annotation of a sequence
  • 3. Transitioning to Genome Compiler
    • 3.1. Vector NTI Express Designer
      • 3.1.1. Transfer your data from vector NTI to Genome Compiler
        • 3.1.1.1. Transferring DNA/RNA molecules
        • 3.1.1.2. Transferring Protein molecules
        • 3.1.1.3. Transferring Single/Multiple oligos
      • 3.1.2. Databases
      • 3.1.3. Abstraction layers
      • 3.1.4. Project Properties
      • 3.1.5. Search in Project
      • 3.1.6. Entrez Search
      • 3.1.7. Workgroup Shared Database
      • 3.1.8. Ordering and Pricing
      • 3.1.9. Back Translation
      • 3.1.10. Designer Project
      • 3.1.11. Restriction Analysis
      • 3.1.12. Primer Design
      • 3.1.13. Clone2Seq
      • 3.1.14. Exo/Fill In/Ligation (Gibson) assembly
      • 3.1.15. ORF Finder
      • 3.1.16. Contig Assembly
      • 3.1.17. Feature Map
      • 3.1.18. Thermodynamics
      • 3.1.19. Adding new parts
    • 3.2. Vector NTI Advance
      • 3.2.1. Transfer your data from vector NTI to Genome Compiler
        • 3.2.1.1. Transferring DNA/RNA molecules
        • 3.2.1.2. Transferring Protein molecules
        • 3.2.1.3. Transferring Single/Multiple oligos
      • 3.2.2. Databases
      • 3.2.3. Abstraction layers
      • 3.2.4. Project Properties
      • 3.2.5. Search in Project
      • 3.2.6. Entrez Search
      • 3.2.7. Workgroup Shared Database
      • 3.2.8. Ordering and Pricing
      • 3.2.9. Back Translation
      • 3.2.10. Designer Project
      • 3.2.11. Restriction Analysis
      • 3.2.12. Primer Design
      • 3.2.13. Clone2Seq
      • 3.2.14. ORF Finder
      • 3.2.15. Contig Assembly
      • 3.2.16. Feature Map
      • 3.2.17. Thermodynamics
      • 3.2.18. Adding new parts
    • 3.3. ApE
      • 3.3.1. Transfer your data from ApE to Genome Compiler
        • 3.3.1.1. Transferring DNA/RNA molecules
        • 3.3.1.2. Transferring Protein molecules
        • 3.3.1.3. Transferring Single/Multiple oligos
      • 3.3.2. Abstraction layers
      • 3.3.3. Search in Project
      • 3.3.4. Entrez Search
      • 3.3.5. Annotate Features Using Library
      • 3.3.6. Restriction Analysis
      • 3.3.7. Primer Design
      • 3.3.8. ORF Detection
      • 3.3.9. Sequence Alignment
      • 3.3.10. Features Table
      • 3.3.11. Thermodynamics
      • 3.3.12. Adding new parts
      • 3.3.13. Windows vs Tabs
      • 3.3.14. Reverse Complement
      • 3.3.15. New Feature
      • 3.3.16. BLAST sequences At NCBI
    • 3.4. SnapGene
      • 3.4.1. Transfer your data from SnapGene to Genome Compiler
        • 3.4.1.1. Transferring DNA/RNA molecules
        • 3.4.1.2. Transferring Protein molecules
        • 3.4.1.3. Transferring Single/Multiple oligos
      • 3.4.2. Abstraction layers
      • 3.4.3. Description Panel
      • 3.4.4. Find
      • 3.4.5. Import from GenBank
      • 3.4.6. Detect common features
      • 3.4.7. Restriction Analysis
      • 3.4.8. Primer Design
      • 3.4.9. Show translation
      • 3.4.10. Align multiple sequences
      • 3.4.11. Features Tab
      • 3.4.12. Thermodynamics
      • 3.4.13. Adding new parts
      • 3.4.14. Windows vs Tabs
      • 3.4.15. Reverse Complement
      • 3.4.16. New Feature
      • 3.4.17. BLAST sequences At NCBI
      • 3.4.18. Files and Folders
      • 3.4.19. Online Resources
      • 3.4.20. Restriction cloning
      • 3.4.21. Gibson Assembly Wizard
  • 4. Introduction
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Genome Compiler Manual