G2KO Files

G2KO is a tool developed by Metabolic Systems Biology Laboratory, IIT Mandi, India

Dependencies:
1. Tool is implemented using perl so installation of latest version perl language is required for the tool to run. Perl is included with most distributions of MacOS and linus. For windows, perl can be downloaded from https://www.activestate.com/products/activeperl/downloads/
2. Internet access is required to download data from KEGG.


How to run the tool:

Step 1.	If you have three/four letter organism KEGG code for upto 10 organisms run 'G2KO.pl' and skip to step 3.
Step 2.	If you don't have organism code, check it in the "Organism.txt" file provided with the package. To update the file, run 'getorg.pl'. This will get the organism list from KEGG database and update the "Organism.txt" file. Organism of interest can be searched in the "Organism.txt" file and corresponding code can be obtained.
Step 3. Open command line in the G2KO tool folder.
(For windows - hold down the Shift key and right click inside the folder. In the menu, you will see the option to 'Open command window here'. More details - https://www.thewindowsclub.com/how-to-open-command-prompt-from-right-click-menu)
(For linux - Right click inside the folder. In the menu, you will see the option to 'Open in terminal')
(For MacOS - Simply drag the G2KO tool folder to the 'Terminal' icon. More details and other method- https://lifehacker.com/launch-an-os-x-terminal-window-from-a-specific-folder-1466745514)
Step 4.	Run command  'perl G2KO.pl' to compare upto 10 organisms. 
Step 5.	Input the organism code and organism name as asked by the tool.
Step 6.	The output for all the organisms is generated in the "outfile.txt' file.
Step 7.	This 'outfile.txt' file can be used as input for KEGG pathway reconstruct tool. KEGG pathway reconstruct is available at https://www.genome.jp/kegg/tool/map_pathway.html

Contact:
Chandrakant Joshi
chandrakant.iitmandi@gmail.com
Metabolic Systems Biology Laboratory, IIT Mandi
Himachal Pradesh 175001
7415292666