Table 3

Comparison of computational time and bowtie mapping

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


# Dataset: PAR-CLIP data from Hafner et. al. (

    SRX020783
).

# Bowtie parameter: one mismatch in miRTarCLIP and two mismatch in PARalyzer.

# System: Linux x64, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 16G RAM.

Chou et al. BMC Genomics 2013 14(Suppl 1):S2   doi:10.1186/1471-2164-14-S1-S2

Open Data