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Table 3 Comparison of computational time and bowtie mapping

From: A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing

 

miRTarCLIP

PARalyzer

Comparison

Times (sec)

C to T program

11.7

-

 

Bowtie

135

301.7

 

Total

146.7

301.7

2 folds

Bowtie input and output

Input reads

6429483

919698

7 folds

Output reports

10785713

16895608

0.64 folds

  1. # Dataset: PAR-CLIP data from Hafner et. al. (SRX020783).
  2. # Bowtie parameter: one mismatch in miRTarCLIP and two mismatch in PARalyzer.
  3. # System: Linux x64, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 16G RAM.
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BMC Genomics

ISSN: 1471-2164

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