I have an entirely new genome of a plant at my hand and I want to predict the protein dominance in it and study the PPI in it.
What would be the best strategy for achieving this? I am naive to this field.
My suggestion to you would be to read two recent reviews - one about plant genomes, and the other about protein-protein interactions. Then read recent papers about each topic; the more papers and review articles you read, the better for you. HTH.
The biggest suggestion I can make is to narrow down your question - a lot. Right now, you are at best looking at a proteomics study: analyze all the proteins, find out how much of each there is. Which, if that's what you want, that's fine. But if not: I'd tend to look at similar plants, pick a couple of important proteins THOSE contain, and see how your own plant compares. If you want protein-protein interactions, presumably you're only going to care about the PPI around a few key targets.
As for PREDICTING protein dominance... I doubt you can. If you have an 'entirely new genome' then, by definition, there's not much data on it, and nothing reliable to predict from. You're really looking more at wet work than computational predictions here.
Dear Aasim,
Please have a look at this useful link and PDF attachments.
https://www.researchgate.net/post/How_to_determine_direct_protein-protein_interaction2/1
Good luck
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