ConSite: web-based prediction of regulatory elements using cross-species comparison

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52. doi: 10.1093/nar/gkh372.


ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/

MeSH terms

  • Animals
  • Binding Sites
  • Conserved Sequence
  • DNA / chemistry*
  • DNA / metabolism
  • DNA Footprinting
  • Internet
  • Phylogeny
  • Regulatory Sequences, Nucleic Acid*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Software*
  • Transcription Factors / metabolism*


  • Transcription Factors
  • DNA