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Table 4 Effect of mismatches and wild cards on search times

From: Suffix tree searcher: exploration of common substrings in large DNA sequence sets

Sequence

Mismatches

Hits

Search time

agtcagtactgga

0

2

461 ms

 

1

61

1.4 s

 

2

1075

1.8 s

 

3

12543

6.8 s

 

4

98684

18.9 s

agtcagtac*gga

0

4

28 ms

 

1

234

1.4 s

 

2

3757

2.5 s

 

3

39076

8.6 s

 

4

277422

33.0 s

agt*agtac*gga

0

30

76 ms

 

1

807

5.9 s

 

2

12777

6.4 s

 

3

118420

17.4 s

 

4

754861

84.3 s

agt*agtac*g*a

0

93

94 ms

 

1

2923

32.7 s

 

2

41372

1 m 0 s

 

3

350292

1 m 27 s

 

4

19708731

2 m 31 s

  1. Searches were performed on trees constructed from a dataset of 10,000 randomly-generated 10 kbp sequences.
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BMC Research Notes

ISSN: 1756-0500

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