DNA assembly protocol generator | TeselaGen's Manual
  • Introduction
  • 1. Intro. to BioCAD/CAM
    • 1.1. From specification, to design, to implementation, to assay
  • 2. Intro. to DNA Assembly
    • 2.1. The DNA assembly challenge
    • 2.2. The traditional multiple cloning site approach
    • 2.3. The BioBrick approach
    • 2.4. The SLIC, Gibson, CPEC and SLiCE assembly methods (and GeneArt Seamless Cloning)
    • 2.5. The Golden Gate assembly method (and MoClo and GoldenBraid)
  • 3. Synthetic Evolution
    • 3.1. TeselaGen's Synthetic Evolution Workflow
    • 3.2. Bioinformatics and BioCAD preliminaries
  • 4. BioCAD demos
    • 4.1. DNA Sequence and Part Management
    • 4.2. Sequence Editing and Part Creation
    • 4.3. Designing with Device Editor
    • 4.4. Generating assembly instructions with J5
  • 5. Managing DNA sequences
    • 5.1. Importing DNA sequences into your sequence library
    • 5.2. Creating a sequence
    • 5.3. Editing a sequence
    • 5.4. Sequence analysis tools
    • 5.5. Mapping sequence to parts
  • 6. Managing columns
    • 6.1. Adding and removing columns
    • 6.2. Changing column SBOL Visual icons
    • 6.3. Changing column assembly orientations
    • 6.4. Changing column names
    • 6.5. Controlling column assembly directives for j5
    • 6.6. Changing the assembly product type (circular-linear)
  • 7. Managing specific parts
    • 7.1. Editing a part's name or definition
    • 7.2. Changing the assembly strategy for a part
    • 7.3. Creating Eugene design specification rules
    • 7.4. Importing a set of Eugene design specification rules
    • 7.5. Cutting, copying, pasting parts
  • 8. Design files
    • 8.1. DeviceEditor format (.xml) design files
  • 9. DNA assembly protocol generator
    • 9.1. Bioinformatics/BioCAD prerequisites to SLIC/Gibson/CPEC/SLiCE and Golden Gate DNA assembly
    • 9.2. Process flow for j5 and integration with Registries of Biological Parts and BioCAD tools
    • 9.3. Brief survey of j5 functionality
  • 10. Specific examples of using j5
    • 10.1. SLIC, Gibson, CPEC assembly (and GeneArt® Seamless Cloning)
    • 10.2. Combinatorial SLIC, Gibson, CPEC assembly
    • 10.3. Mock assembly
    • 10.4. Combinatorial Mock assembly
    • 10.5. Golden Gate assembly
    • 10.6. Combinatorial Golden Gate assembly
    • 10.7. Condensation of multiple j5 assembly files
    • 10.8. Distribution of PCR reactions
    • 10.9. Conversion of SBOL XML <-> GenBank sequence files
  • 11. File formats used by j5
    • 11.1. Comma separated value (.csv); FASTA (.fas) and Genbank (.gb) sequence files
    • 11.2. jbei-seq format (.xml) sequence files
    • 11.3. SBOL XML format (.xml) sequence files
  • 12. j5 input files
    • 12.1. j5 parameters file
    • 12.2. Sequences list file and zipped sequences file
    • 12.3. Parts list file
    • 12.4. Target part order list file
    • 12.5. Eugene rules list file
    • 12.6. Master plasmids list file
    • 12.7. Master oligos list file
    • 12.8. Master direct syntheses list file
    • 12.9. Assembly files to condense list file and zipped assembly files file
    • 12.10. Downstream automation parameters file
    • 12.11. Multi-well plate file
    • 12.12. Source plate list file and zipped source plate files file
  • 13. j5 output assembly files
    • 13.1. SLIC/Gibson/CPEC/SLiCE assembly output file
    • 13.2. Combinatorial SLIC/Gibson/CPEC/SLiCE assembly output file
    • 13.3. Mock Assembly output file
    • 13.4. Combinatorial Mock Assembly output file
    • 13.5. Golden Gate assembly output file
    • 13.6. Combinatorial Golden Gate assembly output file
    • 13.7. Condensed multiple j5 assembly files
  • 14. j5 downstream automation
    • 14.1. Distribute PCR reactions file
    • 14.2. NextGen (eXeTek) expression workstation control file
    • 14.3. PR-PR distribute PCR reactions configuration (.pr) files
  • 15. j5 error messages
    • 15.1. j5 input error messages
    • 15.2. SLIC/Gibson/CPEC/SLiCE or Golden Gate specific error messages
    • 15.3. Distribute PCR Reactions specific error messages
    • 15.4. Condense multiple j5 assembly files specific error messages
    • 15.5. Internal error messages
  • 16. Experimental protocols
    • 16.1. SLIC
    • 16.2. Gibson
    • 16.3. CPEC
    • 16.4. SLiCE
    • 16.5. Golden Gate
    • 16.6. 5' phosphorylation of annealed DNA oligos
  • 17. Related publications
    • 17.1. How to cite j5, and publications citing j5
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TeselaGen's Manual

9. DNA assembly protocol generator

9.1 Bioinformatics/BioCAD prerequisites to SLIC/Gibson/CPEC/SLiCE and Golden Gate DNA assembly
9.2 Process flow for j5 and integration with Registries of Biological Parts and BioCAD tools
9.3 Brief survey of j5 functionality