I'm looking for a method to do an in silico genomic/proteomic analysis to compare the "genetic equipment" of organisms in a way to evaluate their possible abilities to respond to different perturbations.
You could take a look at biocyc.org. There they have taken the genomes of lots of organisms (especially bacteria) and compared them with standard 'reference' organisms (e.g. E. coli) to examine which metabolic pathways are present in which organisms. They have published papers about how they did it: http://biocyc.org/publications.shtml
This is only one possible approach, and there are plenty of alternatives.
Your question has a very wide scope. The broad answer is 'Yes' but there are a lot of detailed questions that make up that answer, and large areas of varying uncertainty. I would say to look up 'homology' and 'orthology', as a starting point to refine your question.
I agree with Reza Shokri. I think this software could well help you.
Sincerely
Behzad
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