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Updated: Aug 21, 2026

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
Published on: June 28, 2018
Promoter prediction analysis on the whole human genome
Vladimir B Bajic1, Sin Lam Tan, Yutaka Suzuki
1Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore. bajicv@i2r.a-star.edu.sg
Abstract:
Promoter prediction programs (PPPs) are important for in silico gene discovery without support from expressed sequence tag (EST)/cDNA/mRNA sequences, in the analysis of gene regulation and in genome annotation. Contrary to previous expectations, a comprehensive analysis of PPPs reveals that no program simultaneously achieves sensitivity and a positive predictive value >65%. PPP performances deduced from a limited number of chromosomes or smaller data sets do not hold when evaluated at the level of the whole genome, with serious inaccuracy of predictions for non-CpG-island-related promoters. Some PPPs even perform worse than, or close to, pure random guessing.
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