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Table 3 Performance comparison of different database sizes for the BAliBASE2-ref7

From: Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

database

# of seqs

SP

TC

extension(s)

total(s)

default T-Coffee

0

0.911

0.498

0

2,735

UniRef50-TM

87,989

0.916

0.561

1,483

8,177

UniRef90-TM

263,306

0.918

0.548

3,343

9,610

UniRef100-TM

613,015

0.925

0.545

6,499

12,111

UniProt-TM

818,635

0.923

0.536

7,871

13,285

UniRef50

3,077,464

0.920

0.553

19,087

26,442

UniRef90

6,544,144

0.924

0.561

40,448

46,478

UniRef100

9,865,668

0.922

0.554

66,696

71,895

UniProt

11,009,767

0.923

0.563

66,964

72,199

NCBI NR

10,565,004

0.921

0.554

65,201

70,375

  1. # of seqs indicates the number of sequences contained in the considered database subset. extension indicates the CPU time required by the homology extension process. total indicates the total CPU time usage.