I don't know how to compare metabolic pathways with their pathway IDs; could you guys please help me?
thank you
As far as I know, differences between metabolic pathways can be analyzed using Petri Nets (but no only limited exclusively to it as it has many other applications as well). For an overview of PetriNets the below link may be useful: http://www.dsi.unive.it/~cocco/Papers/NATC.pdf
For a more specific application of Petri Nets in metabolic pathways see here: http://www.bioinfo.de/isb/gcb99/talks/kueffner/
There is also a different approach, probably a novel one outlined in this paper as well: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.73.651&rep=rep1&type=pdf
If you're not interested in the theoretical methods how metabolic pathways are analyzed, you probably can dive in to these useful tools:
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What kind of metabolic pathways do you mean? Did you get them from a specific source? And what do you want to compare exactly?
there are many ways to 'compare' two pathways. Please provide an example of what you want to achieve.