Combinatorial Mock Assembly
The combinatorial Mock assembly j5 output file is a CSV file that contains all of the information resulting from the combinatorial Mock assembly design process. The first line in the file is a header line that just serves to identify the assembly method selected (e.g. "Combinatorial Mock"), as well as the version of j5 used to generate the assembly (e.g. "v0.1alpha") and the date that the assembly was designed (e.g. "4/7/2010").

"Assembly Parameters" and "Non-degenerate Part IDs and Sources" subsections are identical to those described for the j5 combinatorial SLIC/Gibson/CPEC/SLiCE assembly file.

Note that the "Direct Synthesis", "Oligo Synthesis", "PCR Reactions" and "Assembly Pieces (SLIC/Gibson/CPEC)" sections are not included in combinatorial Mock assembly output files.

Target Bins subsection:
displays the combinatorial target bins.

ID Number column fields:
each combinatorial target bin is enumerated, starting with "0".

Name column fields:
the name of the combinatorial bin, as provided in the target part order list file.

Here is an example Target Bins subsection (stylized for clarity):

Combinations of Parts subsection:
displays which assembly pieces to combine together to generate each of the desired combinatorial variants.

Variant Number column fields:
each assembly combination is enumerated, starting with "0".

Name column fields:
the name of the resulting plasmid for this combination, generated as described in the master plasmids list file documentation section.

Bin N -
Part column fields:
The part contained within bin N for this combinatorial variant.

Here is an example Combinations of Assembly Pieces subsection (stylized for clarity; double-click to see enlarged version):

Example j5 output combinatorial Mock assembly file:
Here is an example j5 combinatorial Mock assembly output CSV file (pGG_00005_combinatorial_mock.csv):