Promoter prediction analysis on the whole human genome

Vladimir Bajic*, Lam Tan Sin, Yutaka Suzuki, Sumio Sugano

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

126 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1467-1473
Number of pages7
JournalNature Biotechnology
Issue number11
StatePublished - Nov 1 2004

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering


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