Table 2

Performance evaluation

Accession number

Query Sequence Length

CBESW (seconds)

CBESW (MCUPS)


O29181

63

18.45

445

P03630

127

19.05

869

P02232

143

19.17

973

P05013

189

19.6

1,258

P14942

222

20.12

1,439

P00762

246

20.24

1,586

P53765

255

20.43

1,628

Q8ZGB4

361

22.04

2,137

P10318

362

22.06

2,141

P07327

374

22.39

2,179

P01008

464

23.18

2,612

P10635

497

23.69

2,737

P58229

511

24.43

2,729

P25705

553

24.74

2,916

P42357

657

26.64

3,218

P21177

729

28.06

3,390

Q38941

850

30.45

3,642

O60341

852

30.49

3,646


Performance evaluation of our implementation, in terms of computational time and MCUPS. All queries were run against Swiss-Prot release 55.2 comprising 130,497,792 amino acids in 362,782 sequence entries. Eighteen query sequences of length 63 to 852 amino acids were used. The gap-open penalty used is 10 and the gap-extension penalty used was 2. The BLOSUM45 scoring matrix was used.

Wirawan et al. BMC Bioinformatics 2008 9:377   doi:10.1186/1471-2105-9-377

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