The panIDs in panYeast-GEM can be replaced with strain-specific genes to result in strain-specific GEMs. Three alternative approaches can be evaluated:
Use getModelFromHomology from RAVEN, where makeFakeBlastStructure converts the panID-gene matches to a structure that can be used by the first function. Drawback is that non-gene associated reactions are not considered, while the advantage is that it can deal well with isoenzymes and subunits.
Use tINIT from RAVEN, where a new function needs to be defined to convert the panID-gene matches to input that can be used by tINIT. Probably the most promising option, but it should be evaluated how it deals with isoenzymes/subunits, and specific tasks should be described that the model should be able to perform.
Write a new independent function, that replaces panIDs with their corresponding strain-specific geneID. Might be just reinventing the wheel with the two options above.
[ ] Evaluate option 1. and 2. and consider whether option 3. could be better.
The panIDs in panYeast-GEM can be replaced with strain-specific genes to result in strain-specific GEMs. Three alternative approaches can be evaluated:
getModelFromHomologyfrom RAVEN, wheremakeFakeBlastStructureconverts the panID-gene matches to a structure that can be used by the first function. Drawback is that non-gene associated reactions are not considered, while the advantage is that it can deal well with isoenzymes and subunits.tINITfrom RAVEN, where a new function needs to be defined to convert the panID-gene matches to input that can be used bytINIT. Probably the most promising option, but it should be evaluated how it deals with isoenzymes/subunits, and specific tasks should be described that the model should be able to perform.