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Table 4 CDD annotations of true positive search results

From: Domain enhanced lookup time accelerated BLAST

   Number and (%) of TPs for which (query, subject)
Method Number of TPs Both match Both match Both match Either matches
   same CD same CDD only different no CD
  superfamily superfamilies  
DELTA-BLAST 51,968 48,612 (93.5) 49,001 (94.3) 2,521 (4.9) 446 (0.9)
PSI-BLAST 45,033 40,194 (89.3) 40,989 (91.0) 3,110 (6.9) 934 (2.1)
BLASTP 16,083 15,769 (98.1) 15,475 (96.2) 437 (2.7) 171 (1.1)
CS-BLAST 21,353 19,791 (92.7) 19,919 (93.3) 1,263 (5.9) 171 (0.8)
Benchmark TPs 196,490 60,663 (30.9) 95,073 (48.4) 88,994 (45.3) 12,423 (6.3)
  1. The columns present: alignment program, number of true positives found, number and percentage of true positives for which a query and a subject both match the same CD, same CDD superfamily, only different CDD superfamilies, and for which either query or subject matches no CD. In the last row, the same data are given for all benchmark true positives.