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Table 3 Classification of paired/orphaned hits for comparative HMMER2 and HMMER3 analysis

From: On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

Group

Classification

Type

Paired hits

HMMER2TRUEHMMER3TRUE

(Positive concordance)

TPTP

  

TPFN

  

FNTP

  

FNFN

 

HMMER2FALSEHMMER3FALSE

(Negative concordance)

TNTN

  

FPTN

  

TNFP

  

FPFP

 

HMMER2TRUEHMMER3FALSE

(Discordance type 1)

TPFP

  

FNFP

  

TPTN

  

FNTN

 

HMMER2FALSEHMMER3TRUE

(Discordance type 2)

FPTP

  

FPFN

  

TNTP

  

TNFN

Orphaned hits

HMMER2ONLY

TP

  

FN

  

FP

  

TN

 

HMMER3ONLY

TP

  

FN

  

FP

  

TN