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Table 2 Traditional TFBS prediction methods and their extensions

From: BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments

Method

Incorporate per-position IC

Incorporate both per-position IC and pair-wise correlation

Consensus

Consensus-IC

Consensus-pair IC

Centroid

Centroid-IC

Centroid-pair IC

Berg and von Hippel

Berg and von Hippel-IC

Berg and von Hippel-pair IC

PSSM

PSSM-IC

PSSM-pair IC

  1. The details of the scoring schemes are described in the report by Signh and coworkers [15]. In our calculation, we use full scope for incorporating pair-wise correlation to the four TFBS prediction methods. IC, information content; PSSM, positional specific scoring matrix; TFBS, transcription factor binding site.