The program needs 3 input files or 4 if using barcodes:
- A file with gene adjustments
- A genbank file with the whole genome
- A genome config file with additional information about the organism.
- Optional: A file with barcode information
Gene operations file¶
The gene operations file is a space or tab separated file. Where every line corresponds to an operation and look as follows:
Gene-Name Operation Options
thiM start_codon_optimal barcodes=ID1+ID2;ID2+ID3 yaaA custom_mutation mut=TATCAACGCC[GCTC=]GCTTTCATGACT,barcodes=ID2 thiC translational_KO KO_frame=10,barcodes=ID1 thiE RBS_library barcodes=ID1 thiF RBS_library max_mutations=5,barcodes=ID3+ID4 thiS RBS_library n=15,passes=3,barcodes=ID1
It is important to notice that there are NO spaces in the options parameter. Any option after a space will be omitted.
Some operations will suppert the genome “gene” as input, such as mutation, deletion and insertion.
Multiple barcodes are supported, they should be separated by a semicolon (;) or a plus (+). Semicolon separated ID’s give multiple oligos with different barcodes, whereas plus separated ID’s result in multiple barcodes on the same oligo.
I.e. thiM in the list above will result in two identical copies of the created oligo, with different barcodes. One with barcodes specified as ID1 and ID2 in the barcode file. And one with ID2 and ID3.
A list of all the operations and corrosponding documentation can be found here: Operations included in MODEST
Genome and genome configuration files¶
MODEST can read genome files in GenBank format (specification). Additional information is however required, such as replication origin/termination.
Genome configuration files (usually ending in .gbcfg), are YAML format text files. MODEST includes tools to generate genome configuration files with minimal input. Read more about Creating your own genome configuration.