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Table 1 Input features to train CoreBoost

From: Boosting with stumps for predicting transcription start sites

Feature list Details
Core promoter elements Score of each core element
Weighted score of pairs between TATA, Inr, and CCAAT- and GC-box
TFBSs Weighted maximal scores for weight matrices from TRANSFAC and density of TFBS
Mechanical properties Weighted energy/flexibility scores around position -25 and +1
Average energy/flexibility scores
Correlation with the empirical average energy/flexibility profile
Markovian score Likelihood ratios from homogeneous third order Markov models
k-mer frequency Frequency of 1- or 2-mers related to nucleotide G or C
  1. TFBS, transcription factor binding site.