The Scientific World Journal

Research Article

Rule-Based Knowledge Acquisition Method for Promoter Prediction in Human and Drosophila Species

Table 1

Conventional features for promoter prediction.
FeaturesLabel
Context features 
  -mere frequencyA1
 TransitionA2
 Distribution A3
 Entropy density profile A4
 Codon-position-independent frequencies of  mononucleotidesA5
 Digitized DNA sequenceA6
 Position-specific informationA7
 Relative entropyA8
 Flanking genomic sequenceA9
Signal features 
 TATAB1
 5′UTR (untranslated region)B2
 Exons regionB3
 Intron regionB4
 3′UTRB5
 Downstream promoter elementB6
 TFIIB recognition element B7
 Motif ten element B8
 CCAATB9
 GCB10
 Transcription factor binding siteC
 CpG islandsD
Structural features 
 DNA curvatureE1
 DNA flexibilityE2
 Stabilizing energy of Z-DNAE3
 DNA denaturation valuesE4
 Base stacking energyE5
 Nucleosome positioning preferenceE6
 Dinucleotide free energyE7
 Tri-nucleotide CG contentE8
 DNA bendabilityE9
 DNA-bending stiffnessE10
 A-philicityE11
 Protein induced deformabilityE12
 Propeller twistE13
 B-DNA twistE14
 Protein-DNA twistE15
 Duplex stability (disrupt energy)E16
 Duplex stability (free energy)E17
 Radical cleavage intensityE18
 Z-DNAE19
Epigenetic featuresF