I have RNA-seq data from a non-model plant and I want to predict and visualize some protein-protein interaction networks -or any other network possible- but I really don't know what is the best server or database to fetch the information about prot-prot interactions.
Can you please share an advice on that matter?
IntAct usually provides more than enough protein-protein interaction data for a good network. It allows for taxonomic breakdown: just search for "species:33090" and you'll get a set of all plant interactions. You may also want to try out mentha (http://mentha.uniroma2.it/). It sources interaction data from a variety of sources (including IntAct) and assigns them reliability scores. The interface can be difficult to work with but the scoring is useful for building a reliable interaction network.