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general:softwares:fcat [2022/11/16 14:08] – [fCAT] 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 - Selected 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 | 
-| Mode 3 - Relaxed mode | The lower bound of the confidence interval calculated by the distribution of all-vs-all FAS score in a core group | Mean of FAS scores between query ortholog and all core proteins |+| Mode 3 - Relaxed mode | The lower bound of the confidence interval calculated by the distribution of all-vs-all FAS score in a core group  | Mean of FAS scores between query ortholog and all core proteins |
 | Mode 4 - Length mode | Mean and standard deviation of all core protein lengths | Length of query ortholog | | Mode 4 - Length mode | Mean and standard deviation of all core protein lengths | Length of query ortholog |
  
-<html><img width="756" alt="image" src="https://user-images.githubusercontent.com/19269760/127915571-6fa4ff00-e5f9-4568-a2c5-520b9c830d25.png"></html>+{{:ecoevo_molevol:wiki:mee:figures:fcat_scoremode.png?600|}}
  
 //Note: **FAS scores** are bidirectional FAS scors; **core protein** or **core ortholog** is protein in the core ortholog groups; **query protein** or **query ortholog** is ortholog protein of query species; **refspec** is the specified reference species// //Note: **FAS scores** are bidirectional FAS scors; **core protein** or **core ortholog** is protein in the core ortholog groups; **query protein** or **query ortholog** is ortholog protein of query species; **refspec** is the specified reference species//