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general:softwares:fcat [2022/11/16 14:18] – [fCAT score modes] vinhgeneral:softwares:fcat [2022/11/16 14:22] (current) – [fCAT score modes] vinh
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 The table below explains how the //specific ortholog group cutoffs// for each fCAT core set were calculated, and which //value of the query ortholog// is used to assess its completeness, or more precisely, its functional equivalence to the ortholog group it belongs to. If the value of a query ortholog is //not less than// its ortholog group cutoff, that group will be evaluated as **similar** or **complete**. In case co-orthologs have been predicted, the assessment for the core group will be **duplicated**. Depending on the value of each single ortholog, a //duplicated// group can be seen as **duplicated (similar)** or **duplicated (dissimilar)** in the full report (e.g. *all_full.txt*). The table below explains how the //specific ortholog group cutoffs// for each fCAT core set were calculated, and which //value of the query ortholog// is used to assess its completeness, or more precisely, its functional equivalence to the ortholog group it belongs to. If the value of a query ortholog is //not less than// its ortholog group cutoff, that group will be evaluated as **similar** or **complete**. In case co-orthologs have been predicted, the assessment for the core group will be **duplicated**. Depending on the value of each single ortholog, a //duplicated// group can be seen as **duplicated (similar)** or **duplicated (dissimilar)** in the full report (e.g. *all_full.txt*).
  
-^ Score mode ^ Cutoff ^ Value ^+^ Score mode ^ Cutoff ^ Value used for comparing ^
 | Mode 1 - Strict mode | Mean of FAS scores between all core orthologs | Mean of FAS scores between query ortholog and all core proteins | | Mode 1 - Strict mode | Mean of FAS scores between all core orthologs | Mean of FAS scores between query ortholog and all core proteins |
 | Mode 2 - Reference mode | Mean of FAS scores between refspec and all other core orthologs | Mean of FAS scores between query ortholog and refspec protein | | Mode 2 - Reference mode | Mean of FAS scores between refspec and all other core orthologs | Mean of FAS scores between query ortholog and refspec protein |