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Table 2 Depicting the sensitivity and specificity analyses of STRIDE compared to PFAM# and TIGRFAM# using 3D7^

From: STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families

  

RIFIN (185)

Non-RIFIN

Predictive value

 

STEVOR (43)

Non-STEVOR

Predictive value

STRIDE

Called + 

182

0

100%

Called + 

38

0

100%

 

Called −

3

5363

100%

Called −

5

5505

99.9%

  

98.4%

100%

  

88.3%

100%

 

PFAM

Called + 

178

0

99%

Called + 

38

0

100%

 

Called −

7

5363

99.8%

Called −

5

5505

99.9%

  

96.2%

99.9%

  

88.3%

100%

 

TIGRFAM

Called + 

177

0

100%

Called + 

38

0

100%

 

Called −

8

5363

99.8%

Called −

5

5505

99.9%

  

95.70%

100%

  

88.3%

100%

 
  1. #We made comparisons across tools using the same parameters as STRIDE
  2. ^The curated 3D7 reference genome served as a gold standard. There are a total of 5548 sequences in the P. falciparum 3D7 reference, where 182 sequences are annotated as RIFINs and 43 sequences are annotated as STEVORs (includes 27 RIFIN and 10 STEVOR pseudogenes). Unlike PFAM and TIGRFAM, STRIDE was not trained with the entire 3D7 RIFIN and STEVOR repertoire (Fig. 2). The bolded text illustrates the sensitivity of each program; all three tools had 100% specificity