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Table 4 Improvements on GLAM 2 's speed and results quality after filtering by TUIUIU

From: Lossless filter for multiple repeats with bounded edit distance

   

TUIUIU

GLAM 2

 

q

d

filter

time(s)

length

time(s)

scrbits

total time (s)

  

no filter

0.00

5518041

125667

262.977

125667

  

FINE*

9.26

264368

4732

244.794

4741

11

7

GOOD*

7.27

109244

2364

303.747

2371

  

EXCELLENT*

9.76

10256

228

283.022

238

  

FINE*

456.55

1556839

36357

287.102

36814

6

12

GOOD*

422.53

221127

5705

356.874

6128

  

EXCELLENT*

439.48

7289

135

469.664

575

  

FINE*

1439.12

4159686

83055

262.977

84494

5

14

GOOD*

1387.27

691442

14545

262.977

15932

  

EXCELLENT*

1499.74

19393

395

406.321

1895

  

FINE*

1640.49

5437974

107908

287.295

109548

5

15

GOOD*

1446.02

3267656

71303

256.076

72749

  

EXCELLENT*

1814.78

375805

7242

268.878

9057

  1. Improvements on GLAM 2's speed and alignment quality after filtering the CFTR dataset with TUIUIU*. Filtration time and final length are provided for the three versions of TUIUIU* with L = 100 and r = 5. Running time, score bits of best multiple alignment found on filtered data is provided for GLAM 2. Tests are done for d = 7, 12, 14, 15 (with respectively q = 11, 6, 5, 5). The last column sums the two time columns, providing the total time (filtering plus alignment).
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Algorithms for Molecular Biology

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