#8 List of core genes

[Ran AJ]

Dear Dr. Chaudhari and Dr. Gupta,

I have a new question about your software BPGA. About the pangenome, can I get the list of the core genes name or their annotation? I would like to know which genes are in the core of my pangenome but I do not find it.

Thank you very much in advance

Best regards,

Rania Assab

[Narendrakumar Chaudhari]

Dear User,

Look for file gi_name in the bin directory after running BPGA analysis. This file contains gene identifiers with their names (if you use gbk or gbff as input). You can just match the accession numbers in Sequences\REPSEQ_core.txt with gi_name to find their names.

Alternatively, if you want the KEGG or COG gene family classification for the same core genome, you can look for K###### numbers or COG#### in Supporting_files\CORE_kegg_hits3.txt or Supporting_files\CORE_COG_hits3.txt, and search online for their names :
For COG numbers - https://ftp.ncbi.nih.gov/pub/COG/COG2014/static/lists/listCOGs.html
For KEGG numbers - https://www.genome.jp/kegg/ko.html (in the text box saying Enter K numbers and click Get title )