Regulatory features | Integrated database or tools | Descriptions |
---|---|---|
Transcriptional start site | NNPP2.2 [14] | Applying a time-delay neural network for promoter annotation |
 | McPromoter [16] | Using a statistical method to identify eukaryotic polymerase II TSS in genomic DNA |
 | Eponine [15] | Predicting the transcription start site for a DNA sequence with prediction specificity > 70% |
Transcription factor (TF) binding site | TRANSFAC public release 7.0 [46] | Storing the experimentally verified transcription factors, their genomic binding sites and DNA-binding profiles |
 | MATCH [29] | Scanning the transcription factor binding site using the transcription factor binding profiles from TRANSFAC public release 7.0 and JASPAR |
CpG island | CpGProD [12] | Detecting the CpG island |
Repeats | TRF [32] | A tandem repeat finder |
TATA box, CCAAT box, and GC box | MATCH [29] | Scanning the TATA-, CCAAT- and GC-box by the transcription factor binding profiles from TRANSFAC |
 | Narang et al. [47] | Defining the 6-mer pattern of the TATA box, CCAAT box, and GX box with positional density |
Over-represented pattern | Huang et al. [48] | Defining the statistically significant pattern in the promoter region |
DNA stability | Aditi Kanhere et al. [21] | Predicting the DNA stability of the promoter region |
Co-occurrence of TF binding sites | apriori [35] | A method to mine the association rules |
Conserved regions between homologous gene promoter sequences | Blast [25] | Using the blast program to analyze the conserved region between the homologous gene promoter sequences |