|
Benchmarking of CpGcluster |
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| Program |
Sn ± SD |
Sp ± SD |
CC ± SD |
Hit* [%] ± SD |
|
|
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| 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. | ||||
Hackenberg et al. BMC Bioinformatics 2006 7:446 doi:10.1186/1471-2105-7-446 |
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