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Table 2 Performance benchmark for ICRPfinder, NEBCutter and WatCut

From: ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

  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*  
  1. 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.
  2. *Only 100 bp were used to run WatCut, since the application limits the length of the input coding sequence to 100 bp.