Files emplacement
GBK, SBML,Scopes files generated from this study and scripts here also input medium (target) file can be found at this address https://zenodo.org/record/4656102#.YGXO5y1h2Bs with DOI: 10.5281/zenodo.4436003.
- All these scripts have been written and drafted first by Enora Geslain. Please also visit this link here https://gitlab.com/Enorya/bacterial_genomes/-/tree/master
1- gbk files are GeneBank format files with all genome information (DNA sequences in a plain text format, metadata, and description) annotated with different pipelines. For example, the quantity of EC numbers can be extracted from this file.
2- Systems Biology Markup Language (SBML) files are manageable file formats for metabolic networks which are generated by Pathway Tool here.
3- scopes files are files containing the compounds which can in principle be synthesized from the initial compounds in the network. These files here are outputs from running MisCoto commands.