I am tasked with finding a pathway solution tool for a commercial environment. This is not my area of expertise and I would appreciate any insight you guys could give.
I am looking for the best tool to integrate bacterial genomes/data to help discover novel activities and microbial pathways. Within this it’s not just creating novel pathway networks, but automatically becoming alerted, when lets say a new publically available genome has genes that match your custom pathway (based upon GO annotation or similar).
It seems on the face of things commercial tools (ingenuity IPA, GENEGO, Pathway studio) are close to what I wish to achieve, but they are very much aimed at pharmaceutical market (databases of drug targets, human genome analysis etc )
How well do these cope with chemicals/intermediates that are not related to drug targets ? or enzymes that may catalyse a related compound using hijacked pathway.
Do they cope well with bacterial pathway analysis?
Even just general pros and cons of software out there would be a big help
Or are there other solutions? Using several tools in combination? PATHologic and metashark look interesting
Any insight, solutions or links to papers/documentation would be great !