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Table 1 Execution time for find_edges variations on a small dataset

From: Compressing DNA sequence databases with coil

Algorithm

Parameters

Execution Time (s)

SSAHA

maxGap = 0,

118.58

 

maxInsert = 0

 
 

maxGap = 20,

118.72

 

maxInsert = 20

 

Basic

 

97.98

Batch merging

c = 16

113.03

 

c = 32

84.35

 

c = 64

71.09

Recursive merging

 

80.55

Hashtable

h = 12

56.02

 

h = 13

56.24

 

h = 14

57.92

  1. The dataset used, month.est_mouse, is a monthly update of the Genbank Mouse EST dataset comprising 31,401 sequences having average length 438 nucleotides.
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BMC Bioinformatics

ISSN: 1471-2105

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