Create a network file to specie without PPI information

Question

[aboutmb]

Hi!

I work with a specie without any PPI information, but I'd like to explore this. So, how is the best way to get that information? I've thought in Blast against A. thaliana, for example. Could anyone please help me?

Thank you so much!

Answer 1

[Leite]

Hello, Olá aboutmb

I was working with goat proteins which is a not very studied animal, so I turned my list to similiar Bos taurus proteins which is the most studied ruminant (via uniprot) and so I built my network in STRING.

Example: You can to do is to turn your list into a list of the most studied Plant and so try to build your network by similarity. Tip: Look at the uniprot list which Plant are present, then convert your list.

Best Regards,

Leite

[Jean-Karim Heriche]

To complete this answer, the general approach is to transfer interactions between orthologs (simply using best blast hits is not very reliable). You don't have to limit yourself to one closely related species.

[aboutmb]

Thank you so much, guys! It worked!