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Table 2 Experiment results of execution time (s) and speedup (Sp) on different platforms for four protein databases with different scale.

From: FPGA accelerator for protein secondary structure prediction based on the GOR algorithm

Test Platforms

gbenv6.fsa_aa

gbcon113.fsa_aa

rsnc.0525.2010.faa

env_nr

 

Time

Speedup

Time

Speedup

Time

Speedup

Time

Speedup

AMD(1)

8.02

1

24.81

1

392.81

1

4308.66

1

Intel(2)

5.11

1.56

16.28

1.52

270.66

1.45

3161.54

1.36

FPGA(3)

0.12

66.8

0.14

177.2

0.91

430.6

9.81

439.2

  1. The hardware experimental environment of different platforms are listed as follows.
  2. AMD(1): Phenom 9650 Quad CPU, 2.3GHz, 3.0GB memory;
  3. Intel(2): Core2 Duo E7400 CPU, 2.8GHz, 3.0GB memory;
  4. FPGA(3): XC5VLX330 FPGA chip, 166MHz, 4.0GB memory.
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BMC Bioinformatics

ISSN: 1471-2105

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