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
User Manual
V.0.6.0
24th August 2015
