MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

Genome Biol. 2004;5(12):R98. doi: 10.1186/gb-2004-5-12-r98. Epub 2004 Nov 30.


We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

Publication types

  • Evaluation Study

MeSH terms

  • Binding Sites
  • Biological Evolution*
  • Conserved Sequence*
  • DNA / metabolism*
  • DNA, Fungal / metabolism
  • DNA-Binding Proteins / metabolism
  • Gene Expression Regulation
  • Models, Genetic
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sequence Alignment*
  • Software*
  • Species Specificity
  • Transcription Factors / metabolism*


  • DNA, Fungal
  • DNA-Binding Proteins
  • GAL4 protein, S cerevisiae
  • RPN4 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • DNA