Table 3 Protocols used to characterize PUFs
Name | Objective | Filters (checked boxes only)a |
|---|---|---|
Protocol A | Find PUFs from organisms whose proteins are not yet in the NCBI’s “nr” database and have no protein domain signatures found by InterproScan | Analyses: no diamond matches Analyses: no interproscan matches |
Protocol B | The same as A but trying to select proteins with the DUF domains from PFAM | Analyses: no diamond matches Analyses: interproscan matches Text search: “Unknown function” |
Protocol C | Find PUFs from organisms whose proteins are already public in the “nr” database | Analyses: diamond matches Analyses: no interproscan matches Text search: “Unknown function” |
Protocol D | Same as A but using ortholog groups and co-expression networks to relate proteins to abiotic stress | Analyses: no diamond matches Analyses: no interproscan matches Orthology: orthology Orthologs_coexpression: co-expression |
Protocol E | Same as B but using ortholog groups and co-expression networks to relate proteins to abiotic stress | Analyses: no diamond matches Analyses: interproscan matches Text search: “Unknown function” Orthology: orthology Orthologs_coexpression: co-expression |
Protocol F | Same as C but using ortholog groups and co-expression networks to relate proteins to abiotic stress | Analyses: diamond matches Analyses: no interproscan matches Text search: “Unknown function” Orthology: orthology Orthologs_coexpression: co-expression |