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Table 2 Comparison of TOFI-alpha and TOFI-beta for the F. tularensis genome on 74 processors

From: A high-throughput pipeline for designing microarray-based pathogen diagnostic assays

   TOFI-alpha TOFI-beta
Stage Step Time Output Time Output
1 MUMmer with near-neighbor 1 m 1730 candidates, 1889863 bp 1 m 1730 candidates, 1889863 bp
1 MUMmer with Proteobacteria - - 8 m 1882 candidates, 1768235 bp
1 MUMmer with nt database - - 23 m 2140 candidates 1192259 bp
2 OMP 2 m 33299 probes 2 m 18668 probes
3 bl2seq with near-neighbor - - 5 m 6979 probes
3 BLAST with Proteobacteria - - 1 hr 37 m 3380 probes
3 BLAST with nt database 22 hrs 1469 fingerprints 2 hrs 13 m 1469 fingerprints
  Total execution time 22 hrs   4 hrs 29 m  
  1. For both TOFI-alpha and TOFI-beta, T = 9 is used as the sole specificity criterion.