How can I specify my proteins gene to orthoMCL

Question

[Esaie]

I'm using orthoMCL, all work fine. But i dont know how to specify to orthoMCL which proteins belong to which genes and to which species. I have searched over Internet i have not seen anything Tank you.

[pooja.singh09]

Did you find the answer to this? I am also search for how to format the gene --> mapping and feed it into the program.

Answer 1

[natasha.sernova]

See this paper: Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196566/

“How the tool processes your proteins: This protocol maps your proteins to groups in OrthoMCL-DB. To understand how OrthoMCL-DB is created, please see the OrthoMCL- DB Methods page.”

OrthoMCL Algorithm:

https://docs.google.com/document/d/1RB-SqCjBmcpNq-YbOYdFxotHGuU7RK_wqxqDAMjyP_w/pub