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Table 3 Running times of PIntron and Exogean on the 26 "critical" genes

From: PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text

Gene

Genomic

length (nt)

Number of

transcripts

Running time (seconds)

   

PIntron

Exogean

ACTB

36,634

26,248

287.35

371.22

ALB

24,299

16,920

144.17

369.38

ANKS1B

1,258,645

406

15.60

0.92

ANXA1

512,535

2,087

20.65

7.63

ATP1A1

619,226

3,241

27.82

11.90

ATP5A1

405,213

9,864

143.33

70.93

CDH13

1,169,823

507

10.34

1.02

CNTNAP2

2,304,964

227

30.86

1.01

CTNNA2

1,463,710

261

12.71

0.96

CUGBP2

1,081,163

864

18.04

2.42

DAB1

1,551,956

164

14.51

0.85

DLG2

2,172,263

279

21.18

1.15

DMD

2,241,933

329

35.35

2.21

ENO1

185,661

13,131

119.84

125.51

FGG

579,042

2,033

15.40

3.56

FHIT (†)

1,502,110

134

202.35

n.a.

GAPDH

46,975

15,518

149.64

232.81

HINT1

873,331

844

12.02

3.08

HSP90AA1

384,611

6,710

47.37

13.87

HSPA8

90,642

15,850

118.47

152.84

KCNIP4

1,220,613

107

10.09

0.65

MBP

154,857

21,071

251.70

1,344.42

NCAM1

317,404

1,293

12.54

1.63

RPL3

187,677

12,208

90.15

108.12

TBC1D22A

1,378,585

467

115.99

2.27

TTN

304,814

1,349

1,952.58

6.77

Total

22,068,686

152,112

3,880.05

2,837.94

  1. † Exogean did not successfully compute a gene structure for FHIT.