iDOG

inter-Domain Operon Generator

Getting Started

This growing suite of tools enables biologists to generate genetic constructs capable of expressing in highly diverse microbial chassis, as outlined in [Jaymin's Paper]. A web interface for these tools is available at [Website]. This github repository provides local command line versions of the RBS generator and Codon Optimizer.

Prerequisites

These scripts are designed to work on UNIX systems, though they have only been tested in Linux. Requirements:

• python (tested on version 3.7)
• python packages:
  • biopython (tested on version 1.7.6)
  • pillow (tested on version 6.2.0)
• Vienna RNA Package (tested on version 2.4.14) Individual programs need to be in path
• A compiled TranstermHP is already provided. This should work for x86 Linux builds. But for arm64 processors, you'll have to recompile from source.

Create a Ribosome Binding Site

Within create_RBS.py, the function create_RBS will design a custom broad host-range RBS

The basic command is as follows:

create_RBS(orf = "", target_tir = "")

where:

• orf is the Nucleotide Sequence of the Open Reading Frame, which must begin with NTG and must be >34bp long
• target_tir is the target Translation Initiation Rate as an integer from 1-999,999. 50,000 is a starting point for overexpression.

optional parameters:

• rRNA_sequence: nucleotide sequence of the presumed 3' end of 16S rRNA. Default: "ACCUCCUUA"
• detailed_output: = True/False. Whether you would like RNA folding plots of the RBS to be outputted. Default: True
• save_url: Directory location where you'd like the detailed output to be stored. Default: ""

Codon Optimize a Gene

Within codon_opt.py, the function codon_opt with recode your gene for broad host-range expression as well as create a companion RBS for the gene

The basic command is as follows:

codon_opt(orf_aa = "", target_tir = "")

where:

• orf_aa is the Amino Acid Sequence of the Open Reading Frame, which must begin with M and must be >13AA lowest_energy
• target_tir is the target Translation Initiation Rate as an integer from 1-999,999. 50,000 is a starting point for overexpression.

optional parameters:

• int_RBS: = True/False. Remove internal RBSs? Default: True
• terminators: = True/False. Remove internal rho-independent transcriptional terminators? Default: True
• species: Base species to use for codon distribution. Default: "escherichia_coli". See section below to add additional organisms
• save_url: Directory location where you'd like the detailed output to be stored. Default ""
• detailed_output: = True/False. Whether you would like RNA folding plots of the RBS, and %GC + RNA Structure plots of the CDS to be outputted. Default: True)

Author

Jaymin Patel (jayman1466@gmail.com)