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Table 3 Search time comparison between Structator' s BIDsearch and an implementation, here called BWI, of bidirectional search using the wavelet tree data structure described in [54].

From: Structator: fast index-based search for RNA sequence-structure patterns

 

hairpin1

hairpin2

hairpin4

hloop(5)

acloop(5)

acloop(10)

BWI

10,484

64

612

26,413

896

420

BIDsearch

8,325

32

330

16,768

511

295

BIDsearch vs. BWI

1.26

2

1.85

1.58

1.75

1.42

  1. Search times are in milliseconds. The last row shows the speedup of BIDsearch over BWI.
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BMC Bioinformatics

ISSN: 1471-2105

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