Table 2

Performance benchmark for ICRPfinder, NEBCutter and WatCut

Details of searching

Response time (sec)

mode

patterns

region

TP53 CDS (1182 bp)

Random CDS (12,000 bp)

ICRPfinder 1

Wild type, Silent mutation

1

Whole coding sequence

0.03

0.21

ICRPfinder 2

Wild type, Silent mutation

2406

Specific region

0.53

0.52

NEBCutter

Wild type

1

Whole coding sequence

3-6

6-12

WatCut

Wild type, Silent mutation

246 (generic enzymes)

Whole coding sequence

2-3*

The performance of ICRPfinder, NEBCutter and WatCut are compared on same data. In the first column ICRPfinder 1 stands for the function to find all potential positions for a specific pattern and ICRPfinder 2 stands for the function to find all unique patterns in a given region.

*Only 100 bp were used to run WatCut, since the application limits the length of the input coding sequence to 100 bp.

Li et al. BMC Bioinformatics 2009 10:286   doi:10.1186/1471-2105-10-286