Table 1.

Benchmarking of CpGcluster

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 (dt = median, or 44 bp)	0.655 ± 0.003	0.976 ± 0.005	0.797 ± 0.009	95.475 ± 0.870
CpGcluster (dt = 75th percentile, or 94 bp)	0.866 ± 0.006	0.832 ± 0.009	0.846 ± 0.006	95.050 ± 0.643

*Hit: Percentage of true islands overlapping (by at least one nucleotide) with predicted islands.

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.