Hej Everybody.
I have catalogue metabolites identified from human seminal plasma. I want to construct metabolite pathway. I have used KEGG. However, most of the metabolite was not in the KEGG. Is the other software I can use for this propose? Any help?
Merci
Pathway analysis is still a tricky business. KEGG offers generic pathways -- sort of a Platonic ideal of what pathways should be -- for a lot of applications, this is not what one might be looking for. BioCyc (https://biocyc.org/) offers community currated pathways -- some are great (I'm looking at you, EcoCyc), but others are not. For human, I always use the commercial systems like IPA.
I suspect other folks will also be able to recommend other good tools.
There are several other good tools out there yes, but many are very cost-prohibitive. Agilent's Mass Profiler Professional does a pretty good job for us, but the database it scans is critical. You mentioned KEGG, but databases like HMDB curate from several other sources, I've found it's better than just KEGG. IPA is very nice, but lots of competitors are out there.
The better ones I've found are the commercial products. You could see if they would give a trial license to see if it's worth your budget?
Pathway Commons might be a place to find something that could work for you as an alternate, but I've not tried anything from there, only recently heard about that group.