Table 3.
Comparison of GPMiner with several representative gene promoter annotation programs
| Transcriptional regulatory features | PromoSer [20] | PromH [49] | DragonGSF [13] | McPromoter [16] | GPMiner |
|---|---|---|---|---|---|
| Species supported | Human, mouse, and rat | Human and mouse | Mammalian | Eukaryote | Human, mouse, rat, chimp, and dog |
| Promoter identification | Yes | Yes | Yes | Yes | Yes |
| Map to known gene promoters | Yes | - | - | - | DBTSS, EPD and Ensembl |
| Transcription factor binding site | - | Yes | Yes | - | TRANSFAC public release and JASPAR, MATCH |
| TATA-box | - | Yes | - | Yes | Yes |
| Tandem repeat | Yes | - | - | Yes | Tandem Repeat Finder |
| CpG island | - | - | Yes | - | CpGProD |
| Over-represented pattern | - | - | - | - | Yes |
| DNA stability | - | - | - | - | Yes |
| GC content | - | - | Yes | - | Yes |
| Co-occurrence of TFBSs | - | Yes | - | - | Yes |
| Graphical view | Yes | - | - | Yes | Yes |