Table 2

Average search time and mean average precision of each program on 108 queries in SCOP-108

Program

Mean of average precision

Total searching time (s)

Average time per query (s)

Related to 3D-BLAST


PSI-BLASTa

69.8%

18.31

0.170

0.533

3D-BLAST

78.2%

34.35

0.318

1

MAMMOTHb

82.1%

131,855

1220.88

3838.58

CE

83.4%

~13.5 days

~3 hours

~34000


Time was measured using a personal computer equipped with an Intel Pentium 2.8 GHz processor with 1,024 megabytes of RAM memory. aPSI-BLAST used E values to rank the hit proteins. bMAMMOTH and CE utilized Z scores to rank hit proteins.

Tung et al. Genome Biology 2007 8:R31   doi:10.1186/gb-2007-8-3-r31

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