Skip to main content

Table 1 Benchmarking of CpGcluster

From: CpGcluster: a distance-based algorithm for CpG-island detection

Program

Sn ± SD

Sp ± SD

CC ± SD

Hit* [%] ± SD

Newcpgreport

0.545 ± 0.002

0.973 ± 0.002

0.725 ± 0.005

87.000 ± 0.540

CpGProD

0.918 ± 0.003

0.657 ± 0.003

0.772 ± 0.006

94.675 ± 0.808

CpGIS

0.832 ± 0.003

0.756 ± 0.007

0.789 ± 0.013

86.675 ± 1.528

CpGIE

0.910 ± 0.002

0.667 ± 0.003

0.775 ± 0.006

94.650 ± 0.810

CpGED

0.819 ± 0.013

0.584 ± 0.004

0.685 ± 0.005

84.075 ± 1.191

CpGcluster (d t = median, or 44 bp)

0.655 ± 0.003

0.976 ± 0.005

0.797 ± 0.009

95.475 ± 0.870

CpGcluster (d t = 75th percentile, or 94 bp)

0.866 ± 0.006

0.832 ± 0.009

0.846 ± 0.006

95.050 ± 0.643

  1. *Hit: Percentage of true islands overlapping (by at least one nucleotide) with predicted islands.
  2. Average accuracy values (Sn, Sp and CC) of CpGcluster and other five CGI finders over 10 test sequences, each one with 400 experimental CGIs. Default parameters values, as recommended in the corresponding publications, were used for each program.